From 7153bd33992c926bb5b5865102ac08e4cef7876f Mon Sep 17 00:00:00 2001 From: Dave B Date: Mon, 10 Jul 2017 11:50:00 -0400 Subject: [PATCH 01/35] Adopt fastx toolkit from devteam. --- .../fasta_clipping_histogram/.shed.yml | 13 ++ .../fasta_clipping_histogram.xml | 103 +++++++++++ .../tool_dependencies.xml | 6 + .../fastx_toolkit/fasta_formatter/.shed.yml | 10 ++ .../fasta_formatter/fasta_formatter.xml | 89 ++++++++++ .../test-data/fasta_formatter1.fasta | 100 +++++++++++ .../test-data/fasta_formatter1.out | 10 ++ .../test-data/fasta_formatter2.out | 84 +++++++++ .../fasta_formatter/tool_dependencies.xml | 6 + .../fasta_nucleotide_changer/.shed.yml | 10 ++ .../fasta_nucleotide_changer.xml | 72 ++++++++ .../test-data/fasta_nuc_change1.out | 50 ++++++ .../test-data/fasta_nuc_change2.out | 50 ++++++ .../test-data/fasta_nuc_changer1.fasta | 50 ++++++ .../test-data/fasta_nuc_changer2.fasta | 50 ++++++ .../tool_dependencies.xml | 6 + .../fastq_quality_boxplot/.shed.yml | 12 ++ .../fastq_quality_boxplot.xml | 57 ++++++ .../fastq_quality_boxplot_1.png | Bin 0 -> 44508 bytes .../fastq_quality_boxplot_2.png | Bin 0 -> 46612 bytes .../fastq_quality_boxplot_3.png | Bin 0 -> 61436 bytes .../tool_dependencies.xml | 6 + .../fastq_quality_converter/.shed.yml | 10 ++ .../fastq_quality_converter.xml | 98 ++++++++++ .../test-data/fastq_qual_conv1.fastq | 36 ++++ .../test-data/fastq_qual_conv1.out | 36 ++++ .../test-data/fastq_qual_conv1a.out | 36 ++++ .../test-data/fastq_qual_conv2.fastq | 60 +++++++ .../test-data/fastq_qual_conv2.out | 60 +++++++ .../test-data/fastq_qual_conv2n.out | 60 +++++++ .../tool_dependencies.xml | 6 + .../fastq_quality_filter/.shed.yml | 10 ++ .../fastq_quality_filter.xml | 83 +++++++++ .../test-data/fastq_qual_filter1.fastq | 36 ++++ .../test-data/fastq_qual_filter1a.out | 4 + .../test-data/fastq_qual_filter1b.out | 24 +++ .../tool_dependencies.xml | 6 + .../fastx_toolkit/fastq_to_fasta/.shed.yml | 11 ++ .../fastq_to_fasta/fastq_to_fasta.xml | 82 +++++++++ .../test-data/fastq_to_fasta1.fastq | 36 ++++ .../test-data/fastq_to_fasta1a.out | 16 ++ .../test-data/fastq_to_fasta1b.out | 18 ++ .../fastq_to_fasta/tool_dependencies.xml | 6 + .../fastx_artifacts_filter/.shed.yml | 11 ++ .../fastx_artifacts_filter.xml | 92 ++++++++++ .../test-data/fastx_artifacts1.fasta | 24 +++ .../test-data/fastx_artifacts1.out | 14 ++ .../test-data/fastx_artifacts2.fastq | 60 +++++++ .../test-data/fastx_artifacts2.out | 40 +++++ .../tool_dependencies.xml | 6 + .../fastx_barcode_splitter/.shed.yml | 11 ++ .../barcode_splitter_output_example.png | Bin 0 -> 46800 bytes .../fastx_barcode_splitter.xml | 73 ++++++++ .../fastx_barcode_splitter_galaxy_wrapper.sh | 80 +++++++++ .../test-data/fastx_barcode_splitter1.fastq | 168 ++++++++++++++++++ .../test-data/fastx_barcode_splitter1.out | 24 +++ .../test-data/fastx_barcode_splitter1.txt | 4 + .../tool_dependencies.xml | 6 + .../fastx_toolkit/fastx_clipper/.shed.yml | 11 ++ .../fastx_clipper/fastx_clipper.xml | 101 +++++++++++ .../fastx_clipper/fastx_clipper_example.png | Bin 0 -> 35053 bytes .../fastx_clipper_illustration.png | Bin 0 -> 10011 bytes .../test-data/fastx_clipper1.fastq | 36 ++++ .../test-data/fastx_clipper1a.out | 8 + .../fastx_clipper_sequences.txt.sample | 13 ++ .../fastx_clipper/tool_dependencies.xml | 6 + .../fastx_toolkit/fastx_collapser/.shed.yml | 10 ++ .../fastx_collapser/fastx_collapser.xml | 90 ++++++++++ .../test-data/fasta_collapser1.fasta | 84 +++++++++ .../test-data/fasta_collapser1.out | 24 +++ .../fastx_collapser/tool_dependencies.xml | 6 + .../fastx_nucleotides_distribution/.shed.yml | 11 ++ .../fastq_nucleotides_distribution_1.png | Bin 0 -> 19899 bytes .../fastq_nucleotides_distribution_2.png | Bin 0 -> 23420 bytes .../fastq_nucleotides_distribution_3.png | Bin 0 -> 23757 bytes .../fastq_nucleotides_distribution_4.png | Bin 0 -> 21360 bytes .../fastx_nucleotides_distribution.xml | 53 ++++++ .../tool_dependencies.xml | 6 + .../fastx_quality_statistics/.shed.yml | 11 ++ .../fastx_quality_statistics.xml | 71 ++++++++ .../test-data/fastq_stats1.fastq | 36 ++++ .../test-data/fastq_stats1.out | 37 ++++ .../tool_dependencies.xml | 6 + .../fastx_toolkit/fastx_renamer/.shed.yml | 11 ++ .../fastx_renamer/fastx_renamer.xml | 70 ++++++++ .../fastx_renamer/tool_dependencies.xml | 6 + .../fastx_reverse_complement/.shed.yml | 12 ++ .../fastx_reverse_complement.xml | 63 +++++++ .../test-data/fastx_rev_comp1.fasta | 4 + .../test-data/fastx_rev_comp2.fastq | 8 + .../test-data/fastx_reverse_complement1.out | 4 + .../test-data/fastx_reverse_complement2.out | 8 + .../tool_dependencies.xml | 6 + .../fastx_toolkit/fastx_trimmer/.shed.yml | 11 ++ .../fastx_trimmer/fastx_trimmer.xml | 83 +++++++++ .../test-data/fastx_trimmer1.fasta | 4 + .../test-data/fastx_trimmer1.out | 4 + .../test-data/fastx_trimmer2.fastq | 8 + .../test-data/fastx_trimmer2.out | 8 + .../fastx_trimmer/tool_dependencies.xml | 6 + 100 files changed, 3067 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tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml new file mode 100644 index 00000000000..8838742c67a --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml @@ -0,0 +1,13 @@ +categories: +- Fasta Manipulation +- Graphics +- Statistics +description: Length Distribution chart +long_description: | + This tool creates a histogram image of sequence lengths distribution + in a given fasta dataset file. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fasta_clipping_histogram +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml new file mode 100644 index 00000000000..7275e20e31d --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -0,0 +1,103 @@ + + chart + + fastx_toolkit + + fasta_clipping_histogram.pl $input $outfile + + + + + + + + + + + +**What it does** + +This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file. + +**TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results. + +----- + +**Output Examples** + +In the following library, most sequences are 24-mers to 27-mers. +This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place). + +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png + +In the following library, most sequences are 19,22 or 23-mers. +This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place). + +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png + +----- + +**Input Formats** + +This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so:: + + >sequence1 + AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG + >sequence2 + GTGTGTGTGGGAAGTTGACACAGTA + >sequence3 + CCTTGAGATTAACGCTAATCAAGTAAAC + +If the sequences span over multiple lines:: + + >sequence1 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG + TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG + aactggtctttacctTTAAGTTG + +Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences:: + + >sequence1 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG + +----- + +**Multiplicity counts (a.k.a reads-count)** + +If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing). + +Example 1 - The following FASTA file *does not* have multiplicity counts:: + + >seq1 + GGATCC + >seq2 + GGTCATGGGTTTAAA + >seq3 + GGGATATATCCCCACACACACACAC + +Each sequence is counts as one, to produce the following chart: + +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png + +Example 2 - The following FASTA file have multiplicity counts:: + + >seq1-2 + GGATCC + >seq2-10 + GGTCATGGGTTTAAA + >seq3-3 + GGGATATATCCCCACACACACACAC + +The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart: + +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png + +Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts. + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml b/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml new file mode 100644 index 00000000000..6c1e37fccf3 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml @@ -0,0 +1,10 @@ +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +categories: +- Fasta Manipulation +description: FASTA Width formatter +long_description: | + This tool re-formats a FASTA file, changing the width of the nucleotides lines. +name: fasta_formatter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_formatter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml new file mode 100644 index 00000000000..52a53ce4426 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml @@ -0,0 +1,89 @@ + + formatter + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool re-formats a FASTA file, changing the width of the nucleotides lines. + +**TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line. + +-------- + +**Example** + +Input FASTA file (each nucleotides line is 50 characters long):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC + CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG + TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA + ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG + TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG + aactggtctttacctTTAAGTTG + + +Output FASTA file (with width=80):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT + ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA + ATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC + GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG + +Output FASTA file (with width=0 => single line):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta new file mode 100644 index 00000000000..3c76807ab38 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta @@ -0,0 +1,100 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC +CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG +TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA +GTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTAT +ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATC +TACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT +TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGC +AAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTT +GATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATA +GCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAG +AAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACT +AAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT +TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAA +AGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAG +AGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCA +ACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTC +GCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATA +CATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT +ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATA +ATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG +TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG +GAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAa +ggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaag +ctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatga +taaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt +gtttctctcatggtctgtgagagatatagggtagtcccatatacatcttt +ctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatca +ttttgatgattccagaaccttgcagatgcgagatggtagatgatcaacct +tttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccat +aactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAG +TTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT +GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGC +CAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAA +AAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGA +AGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGT +GTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAA +ATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT +CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATT +AAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGAT +ATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGT +GTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATA +CTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAG +ATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTA +TGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAAT +TTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATT +AGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTT +TTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAAC +GAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT +ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATC +GAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAAT +ACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAG +TTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAA +TCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAA +TGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt +gataatttttttttctttgataatttttttctttttctttaataaatttt +ttggataatttttttttggataaatagttcttttttgataattctaataa +tttttttatttattttttttttttctataattttttttaaaaaatttatt +aatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGAC +AATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATAC +GCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACT +TTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGA +TGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtg +tgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTG +ATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA +ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgt +gcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATT +GCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAA +AAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAA +CGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAG +AGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA +AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAA +GTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtact +atgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgca +tttgaaagataatactaatttacaacttccctaaaaaaggtggggcttga +aaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactt +tagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAA +GTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGT +ACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttat +atCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctc +tcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACT +TGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT +TTGtctctgttcccctctccccccctctctctctctctctctctctctct +ctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTG +TTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTT +AATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAA +CTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTA +CTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA +GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTT +CTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTG +GACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATA +TTA diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out new file mode 100644 index 00000000000..dab0e10a3e3 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out @@ -0,0 +1,10 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out new file mode 100644 index 00000000000..40fbc313e49 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out @@ -0,0 +1,84 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCA +GGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGG +TATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACA +ACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATA +CATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT +TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAA +AAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATT +CTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGG +CACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGC +CTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT +TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGC +ATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTA +AACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCC +ATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGC +TACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT +ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGT +TCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCA +TAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTT +TCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaat +ttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaa +tacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt +gtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatag +tgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaacct +tgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttca +caatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAA +CACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT +GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAG +AAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTG +AAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAA +AACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAA +ATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT +CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATT +TGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACG +GTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAA +ATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTAT +CCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATA +AACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCA +TTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATG +ATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATT +GTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT +ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATG +ATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTG +GTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTT +GGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCT +GCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt +gataatttttttttctttgataatttttttctttttctttaataaattttttggataatt +tttttttggataaatagttcttttttgataattctaataatttttttatttatttttttt +ttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTA +ACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAA +GACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACA +TTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtg +tgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgt +ACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA +ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgt +gagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCAT +GAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGG +AAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGA +GAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA +AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGC +AGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaa +aaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttcc +ctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtc +aaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTT +TGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCT +GTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttctt +gtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAG +TTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT +TTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctct +ttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTT +GCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGT +TGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATT +ATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA +GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTT +AACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGC +TTTGATGCCAATCCAACAATTTTGCATATATTA diff --git a/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml new file mode 100644 index 00000000000..00e61fb218e --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Fasta Manipulation +description: RNA/DNA converter. +long_description: | + This tool converts RNA FASTA files to DNA (and vice-versa). +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fasta_nucleotide_changer +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml new file mode 100644 index 00000000000..e15c606044b --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -0,0 +1,72 @@ + + converter + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool converts RNA FASTA files to DNA (and vice-versa). + +In **RNA-to-DNA** mode, U's are changed into T's. + +In **DNA-to-RNA** mode, T's are changed into U's. + +-------- + +**Example** + +Input RNA FASTA file ( from Sanger's mirBase ):: + + >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 + UGAGGUAGUAGGUUGUAUAGUU + >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 + UCCCUGAGACCUCAAGUGUGA + >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 + UGGAAUGUAAAGAAGUAUGUA + +Output DNA FASTA file (with RNA-to-DNA mode):: + + >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 + TGAGGTAGTAGGTTGTATAGTT + >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 + TCCCTGAGACCTCAAGTGTGA + >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 + TGGAATGTAAAGAAGTATGTA + + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out new file mode 100644 index 00000000000..e46135f36f4 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +UGAGGUAGUAGGUUGUAUAGUU +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +UCCCUGAGACCUCAAGUGUGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +UGGAAUGUAAAGAAGUAUGUA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +UAUCACAGCCAGCUUUGAUGUGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGUGUGGUUAGCUGGUUG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +UCACCGGGUGGAAACUAGCAGU +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +UCACCGGGUGAAAAUUCGCAUG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +UCACCGGGUGAACACUUGCAGU +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +UCACCGGGAGAAAAACUGGAGU +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +UCACCGGGUGUAAAUCAGCUUG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +UCACCGGGUGUACAUCAGCUAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +UCACCGGGUGAAAAAUCACCUA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +UCACCGGGUUAACAUCUACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +UAUCACAGUUUACUUGCUGUCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +UGACUAGAGACACAUUCAGCU +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +UGACUAGAGACACAUUCAGCU +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +UGUCAUGGAGUCGCUCUCUUCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +UGUCAUGGAGGCGCUCUCUUCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +UGAGGUAGGCUCAGUAGAUGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCUGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +UGAUAUGUCUGGUAUUCUUGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +UACCCGUAGCUCCUAUCCAUGUU +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGUACAUAUGUUUCCGUGCU +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGUACAUUUGUUUCCGUGCU +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +UACCCGUAAUCUUCAUAAUCCGAG diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out new file mode 100644 index 00000000000..c42d9dc113f --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +TGAGGTAGTAGGTTGTATAGTT +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +TCCCTGAGACCTCAAGTGTGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +TGGAATGTAAAGAAGTATGTA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +TATCACAGCCAGCTTTGATGTGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGTGTGGTTAGCTGGTTG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +TCACCGGGTGGAAACTAGCAGT +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +TCACCGGGTGAAAATTCGCATG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +TCACCGGGTGAACACTTGCAGT +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +TCACCGGGAGAAAAACTGGAGT +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +TCACCGGGTGTAAATCAGCTTG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +TCACCGGGTGTACATCAGCTAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +TCACCGGGTGAAAAATCACCTA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +TCACCGGGTTAACATCTACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +TATCACAGTTTACTTGCTGTCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +TGACTAGAGACACATTCAGCT +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +TGACTAGAGACACATTCAGCT +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +TGTCATGGAGTCGCTCTCTTCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +TGTCATGGAGGCGCTCTCTTCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +TGAGGTAGGCTCAGTAGATGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCTGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +TGATATGTCTGGTATTCTTGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +TACCCGTAGCTCCTATCCATGTT +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGTACATATGTTTCCGTGCT +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGTACATTTGTTTCCGTGCT +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +TACCCGTAATCTTCATAATCCGAG diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta new file mode 100644 index 00000000000..c42d9dc113f --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +TGAGGTAGTAGGTTGTATAGTT +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +TCCCTGAGACCTCAAGTGTGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +TGGAATGTAAAGAAGTATGTA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +TATCACAGCCAGCTTTGATGTGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGTGTGGTTAGCTGGTTG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +TCACCGGGTGGAAACTAGCAGT +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +TCACCGGGTGAAAATTCGCATG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +TCACCGGGTGAACACTTGCAGT +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +TCACCGGGAGAAAAACTGGAGT +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +TCACCGGGTGTAAATCAGCTTG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +TCACCGGGTGTACATCAGCTAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +TCACCGGGTGAAAAATCACCTA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +TCACCGGGTTAACATCTACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +TATCACAGTTTACTTGCTGTCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +TGACTAGAGACACATTCAGCT +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +TGACTAGAGACACATTCAGCT +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +TGTCATGGAGTCGCTCTCTTCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +TGTCATGGAGGCGCTCTCTTCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +TGAGGTAGGCTCAGTAGATGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCTGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +TGATATGTCTGGTATTCTTGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +TACCCGTAGCTCCTATCCATGTT +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGTACATATGTTTCCGTGCT +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGTACATTTGTTTCCGTGCT +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +TACCCGTAATCTTCATAATCCGAG diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta new file mode 100644 index 00000000000..e46135f36f4 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +UGAGGUAGUAGGUUGUAUAGUU +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +UCCCUGAGACCUCAAGUGUGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +UGGAAUGUAAAGAAGUAUGUA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +UAUCACAGCCAGCUUUGAUGUGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGUGUGGUUAGCUGGUUG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +UCACCGGGUGGAAACUAGCAGU +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +UCACCGGGUGAAAAUUCGCAUG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +UCACCGGGUGAACACUUGCAGU +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +UCACCGGGAGAAAAACUGGAGU +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +UCACCGGGUGUAAAUCAGCUUG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +UCACCGGGUGUACAUCAGCUAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +UCACCGGGUGAAAAAUCACCUA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +UCACCGGGUUAACAUCUACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +UAUCACAGUUUACUUGCUGUCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +UGACUAGAGACACAUUCAGCU +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +UGACUAGAGACACAUUCAGCU +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +UGUCAUGGAGUCGCUCUCUUCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +UGUCAUGGAGGCGCUCUCUUCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +UGAGGUAGGCUCAGUAGAUGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCUGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +UGAUAUGUCUGGUAUUCUUGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +UACCCGUAGCUCCUAUCCAUGUU +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGUACAUAUGUUUCCGUGCU +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGUACAUUUGUUUCCGUGCU +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +UACCCGUAAUCUUCAUAAUCCGAG diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml new file mode 100644 index 00000000000..cd52b7af998 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Fastq Manipulation +- Graphics +- Statistics +description: Draw quality score boxplot +long_description: | + Creates a boxplot graph for the quality scores in the library. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastq_quality_boxplot +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml new file mode 100644 index 00000000000..2c76a645fde --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml @@ -0,0 +1,57 @@ + + + + fastx_toolkit + + fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output + + + + + + + + + + +**What it does** + +Creates a boxplot graph for the quality scores in the library. + +.. class:: infomark + +**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. + +----- + +**Output Examples** + +* Black horizontal lines are medians +* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1) +* Whiskers show outlier at max. 1.5*IQR + + +An excellent quality library (median quality is 40 for almost all 36 cycles): + +.. image:: fastq_quality_boxplot_1.png + + +A relatively good quality library (median quality degrades towards later cycles): + +.. image:: fastq_quality_boxplot_2.png + +A low quality library (median drops quickly): + +.. image:: fastq_quality_boxplot_3.png + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_1.png b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_1.png new file mode 100644 index 0000000000000000000000000000000000000000..f721716a18cf42e5a5e7e534daeeeb17e028bf95 GIT binary patch literal 44508 zcmaI7Wmp?uw8jgC;sjbK?i6<^8iKo|Kyh~{?ry~$3dOBxDNb>3a47EX?!ojs(?rO@+HYoMAC&2fl<`# 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b/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Fastq Manipulation +description: Quality format converter (ASCII-Numeric) +long_description: | + Converts a Solexa FASTQ file to/from numeric or ASCII quality format. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastq_quality_converter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml new file mode 100644 index 00000000000..c143cb89b94 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml @@ -0,0 +1,98 @@ + + (ASCII-Numeric) + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Converts a Solexa FASTQ file to/from numeric or ASCII quality format. + +.. class:: warningmark + +Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). + +----- + +FASTQ with Numeric quality scores:: + + @CSHL__2_FC042AGWWWXX:8:1:120:202 + ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC + +CSHL__2_FC042AGWWWXX:8:1:120:202 + 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 + @CSHL__2_FC042AGWWWXX:8:1:103:1185 + ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC + +CSHL__2_FC042AGWWWXX:8:1:103:1185 + 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 + + +FASTQ with ASCII quality scores:: + + @CSHL__2_FC042AGWWWXX:8:1:120:202 + ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC + +CSHL__2_FC042AGWWWXX:8:1:120:202 + hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH + @CSHL__2_FC042AGWWWXX:8:1:103:1185 + ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC + +CSHL__2_FC042AGWWWXX:8:1:103:1185 + hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq new file mode 100644 index 00000000000..76c0d6c4f2a --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACACACACTCATCGTCGTCCCCCG ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACCC ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out new file mode 100644 index 00000000000..73283203055 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +33 33 34 30 22 30 33 21 29 32 33 33 30 33 26 33 33 33 34 34 24 5 26 33 34 33 33 33 33 33 33 33 33 29 29 32 +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC ++CSHL_3_FC042AGLLWW:1:2:7:33 +23 33 33 33 30 33 26 33 33 23 30 21 31 24 33 23 33 33 28 23 13 5 16 30 11 5 26 24 18 16 5 5 5 7 33 33 +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +33 31 13 30 33 28 21 33 33 33 31 13 31 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 22 28 26 21 7 21 21 18 +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +33 30 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 31 21 32 33 33 33 33 33 31 19 31 33 33 33 33 33 22 22 27 +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACACACACTCATCGTCGTCCCCCG ++CSHL_3_FC042AGLLWW:1:2:7:292 +34 33 34 33 33 33 33 33 33 33 21 13 33 33 33 33 33 33 33 33 33 33 33 28 24 5 21 21 5 16 31 29 21 5 18 5 +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACCC ++CSHL_3_FC042AGLLWW:1:2:7:1819 +33 28 28 17 22 22 22 12 33 33 12 15 5 24 21 23 21 21 5 11 21 21 12 5 13 21 5 21 21 11 21 12 9 17 13 21 +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +33 33 33 33 33 33 33 33 33 24 21 24 24 5 24 33 33 33 33 33 32 31 26 33 33 33 33 33 33 33 33 33 24 5 24 21 +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:8:624 +33 33 27 19 30 32 24 32 33 33 31 29 29 15 15 24 13 21 30 31 27 13 21 31 33 33 33 33 33 33 33 33 33 33 33 33 +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT ++CSHL_3_FC042AGLLWW:1:2:8:250 +33 33 33 33 33 33 33 33 30 33 33 33 33 33 33 34 34 34 27 11 24 16 5 21 27 18 24 26 30 10 21 11 18 11 24 5 diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out new file mode 100644 index 00000000000..76c0d6c4f2a --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACACACACTCATCGTCGTCCCCCG ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACCC ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq new file mode 100644 index 00000000000..e3caaf2d9f2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq @@ -0,0 +1,60 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1601:1525 +40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1713:528 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1236:1157 +40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 +@CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1818:550 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 +@CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC0420AGLLKK:2:1:1764:391 +40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out new file mode 100644 index 00000000000..56cb36d4af0 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out @@ -0,0 +1,60 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +hhhhhhhhhhhhhhhhhh`hhhhPTYIUehhP]Z^ +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +hhhhhhhhhhhhhhhhhhhhhhh;MQ\hhHQ[HMJ +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +hhhhhhhhhhhhhhhDhhZchfhFhh@CZ`[NKZK +@CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1601:1525 +hhhhhhhhhhhhchhLhh^^hhhLdWQXRVYOJbN +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +hhhhhhhhhhhhhhhhhPW\hUhIeMTUGKNNFWJ +@CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1713:528 +hhhhhhhhhhhhhhhhhhhhh`hLfOVTQNLJGVK +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +hhhhhhhhhhhhhhYhhhhhhh_hhKJWhMLQeQV +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +hhhhhhhhhhhhhhhhhhgV_hhL]V@GLHRGCRI +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +hhghhhhhhhhhDhhXbTaUd`h;hMUUZQRYNYU +@CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1236:1157 +hhhhhhhhhhhhhchhhhhahehhhRPTWV_ZJVS +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +hhhhhhhhhhhhhY[hec[hhQh;dKSOSPKLLWK +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +hhhhhhhhhhhhhhhhhhhhhh^hhXRfaZPWVPR +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +hhhhhhhhchghh[ThQbOhhhhO\QDLJJRNCNK +@CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1818:550 +hhhhhhhhhhhhhhd`hahhfeh\][VMTSQQMaR +@CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC0420AGLLKK:2:1:1764:391 +hhhhhhhhhhhahhhhhXhhhhhLhXNIVO]RKhV diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out new file mode 100644 index 00000000000..e3caaf2d9f2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out @@ -0,0 +1,60 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1601:1525 +40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1713:528 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1236:1157 +40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 +@CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1818:550 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 +@CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC0420AGLLKK:2:1:1764:391 +40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml new file mode 100644 index 00000000000..e4cd18d8c65 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Fastq Manipulation +description: Filter by quality +long_description: | + This tool filters reads based on quality scores. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastq_quality_filter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml new file mode 100644 index 00000000000..ba360c7f63c --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -0,0 +1,83 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool filters reads based on quality scores. + +.. class:: infomark + +Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value. + +.. class:: infomark + +Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value. + +-------- + +Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded. + + +**Example**:: + + @CSHL_4_FC042AGOOII:1:2:214:584 + GACAATAAAC + +CSHL_4_FC042AGOOII:1:2:214:584 + 30 30 30 30 30 30 30 30 20 10 + +Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30). + +Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30). + +Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq new file mode 100644 index 00000000000..ea3db077f2e --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +aaaaaaaaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out new file mode 100644 index 00000000000..f274daf1c83 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out @@ -0,0 +1,4 @@ +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out new file mode 100644 index 00000000000..6353aded69b --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml b/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml new file mode 100644 index 00000000000..84f26dfc3e8 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Convert Formats +description: FASTQ to FASTA converter +long_description: | + This tool converts data from FASTQ format to FASTA format. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastq_to_fasta +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml new file mode 100644 index 00000000000..410aa0222b8 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -0,0 +1,82 @@ + + converter from FASTX-toolkit + + fastx_toolkit + + gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v +#if $input.ext == "fastqsanger": +-Q 33 +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool converts data from Solexa format to FASTA format (scroll down for format description). + +-------- + +**Example** + +The following data in Solexa-FASTQ format:: + + @CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +CSHL_4_FC042GAMMII_2_1_517_596 + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +Will be converted to FASTA (with 'rename sequence names' = NO):: + + >CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +Will be converted to FASTA (with 'rename sequence names' = YES):: + + >1 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq new file mode 100644 index 00000000000..d3386dda038 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out new file mode 100644 index 00000000000..c524fd4e12a --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out @@ -0,0 +1,16 @@ +>CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +>CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +>CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT +>CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA +>CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA +>CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +>CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +>CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out new file mode 100644 index 00000000000..c5b35f433d9 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out @@ -0,0 +1,18 @@ +>1 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +>2 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +>3 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +>4 +AATTATTTATTAAATTTTAATAATATGGGAGACACT +>5 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA +>6 +AATTCAAACCACCCCAACCCACACACAGAGATACAA +>7 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +>8 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +>9 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml new file mode 100644 index 00000000000..e0d7e71a27e --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Remove sequencing artifacts +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +long_description: | + This tool filters sequencing artifacts (reads with all but 3 identical bases). +name: fastx_artifacts_filter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml new file mode 100644 index 00000000000..4f7505f5b85 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -0,0 +1,92 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool filters sequencing artifacts (reads with all but 3 identical bases). + +-------- + +**The following is an example of sequences which will be filtered out**:: + + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA + AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA + AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA + AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta new file mode 100644 index 00000000000..bd848fd4b27 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta @@ -0,0 +1,24 @@ +>CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA +>CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +>CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA +>CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA +>CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +>CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA +>CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out new file mode 100644 index 00000000000..77833e34f4d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out @@ -0,0 +1,14 @@ +>CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA +>CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +>CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq new file mode 100644 index 00000000000..e3caaf2d9f2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq @@ -0,0 +1,60 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1601:1525 +40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1713:528 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1236:1157 +40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 +@CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1818:550 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 +@CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC0420AGLLKK:2:1:1764:391 +40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out new file mode 100644 index 00000000000..d82412b46e3 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out @@ -0,0 +1,40 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml new file mode 100644 index 00000000000..69416b9584e --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Barcode Splitter +long_description: | + This tool splits a FASTQ file or a regular FASTA file into several files, using barcodes as the split criteria. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastx_barcode_splitter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/barcode_splitter_output_example.png b/tool_collections/fastx_toolkit/fastx_barcode_splitter/barcode_splitter_output_example.png new file mode 100644 index 0000000000000000000000000000000000000000..c0f8944cc8b2d62829943072d36176c3283467a9 GIT binary patch literal 46800 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z;nZ17xdo`ocn;%7YD>7mH6F7nD&w;FKcv^^S*Cj$wA+K3)ofo88;iMD$;R5tc}Kt* zsSaz_D}DAe2b zU(-RV657Gbl4;j^hYm2tINu!h#$E>zj4fyh6Lb69TIWUNoWAE0);FIbcl*WtQvY^g@r>S(02*!;n7l4 z9Qv0M?bQ>%+Gpl1C-&v^45)axG587ToimxhdNvRI{m$4V3tWPrx>yUhH*7{AYz_gaJ+hWVPS z-BeNbKjhzk-mXJ&A^qzh%FK-ZpSye7g!({b%AmcE!`a;jd_J<0N)pxL#=-v&Iu{+a literal 0 HcmV?d00001 diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml new file mode 100644 index 00000000000..3f627f3dffe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -0,0 +1,73 @@ + + + + fastx_toolkit + + fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. + +-------- + +**Barcode file Format** + +Barcode files are simple text files. +Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. +Example:: + + #This line is a comment (starts with a 'number' sign) + BC1 GATCT + BC2 ATCGT + BC3 GTGAT + BC4 TGTCT + +For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). +Sequences matching the barcode will be stored in the appropriate file. + +One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. + +The output of this tool is an HTML file, displaying the split counts and the file locations. + +**Output Example** + +.. image:: barcode_splitter_output_example.png + + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh new file mode 100755 index 00000000000..976404c99aa --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh @@ -0,0 +1,80 @@ +#!/bin/bash + +# FASTX-toolkit - FASTA/FASTQ preprocessing tools. +# Copyright (C) 2009 A. Gordon (gordon@cshl.edu) +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . + +# +#This is a shell script wrapper for 'fastx_barcode_splitter.pl' +# +# 1. Output files are saved at the dataset's files_path directory. +# +# 2. 'fastx_barcode_splitter.pl' outputs a textual table. +# This script turns it into pretty HTML with working URL +# (so lazy users can just click on the URLs and get their files) + +BARCODE_FILE="$1" +FASTQ_FILE="$2" +LIBNAME="$3" +OUTPUT_PATH="$4" +shift 4 +# The rest of the parameters are passed to the split program + +if [ "$OUTPUT_PATH" == "" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 + exit 1 +fi + +#Sanitize library name, make sure we can create a file with this name +LIBNAME=${LIBNAME//\.gz/} +LIBNAME=${LIBNAME//\.txt/} +LIBNAME=${LIBNAME//[^[:alnum:]]/_} + +if [ ! -r "$FASTQ_FILE" ]; then + echo "Error: Input file ($FASTQ_FILE) not found!" >&2 + exit 1 +fi +if [ ! -r "$BARCODE_FILE" ]; then + echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 + exit 1 +fi +mkdir -p "$OUTPUT_PATH" +if [ ! -d "$OUTPUT_PATH" ]; then + echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 + exit 1 +fi + +PUBLICURL="" +BASEPATH="$OUTPUT_PATH/" +#PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" +PREFIX="$BASEPATH""${LIBNAME}__" +SUFFIX=".txt" + +RESULTS=`zcat -f < "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` +if [ $? != 0 ]; then + echo "error" +fi + +# +# Convert the textual tab-separated table into simple HTML table, +# with the local path replaces with a valid URL +echo "" +echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed ' +i
+s|\t||g +a<\/td><\/tr> +' +echo "

" +echo "

" diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq new file mode 100644 index 00000000000..7cbcf9977bd --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq @@ -0,0 +1,168 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out new file mode 100644 index 00000000000..62baea3e96c --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out @@ -0,0 +1,24 @@ + + + + + + + + +

+

+BarcodeCountLocation +
+BC111fastx_barcode_splitter1_fastq__BC1.txt +
+BC212fastx_barcode_splitter1_fastq__BC2.txt +
+BC39fastx_barcode_splitter1_fastq__BC3.txt +
+BC41fastx_barcode_splitter1_fastq__BC4.txt +
+unmatched9fastx_barcode_splitter1_fastq__unmatched.txt +
+total42 +
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt new file mode 100644 index 00000000000..8a7ba617b8d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt @@ -0,0 +1,4 @@ +BC1 GATCT +BC2 ATCGT +BC3 GTGAT +BC4 TGTCT \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml b/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml new file mode 100644 index 00000000000..85d233f0e30 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Clip adapter sequences +long_description: | + This tool clips adapters from the 3''-end of the sequences in a FASTA/FASTQ file. +name: fastx_clipper +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml new file mode 100644 index 00000000000..2fb04f55e49 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -0,0 +1,101 @@ + + adapter sequences + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + use this for hairpin barcoding. keep at 0 unless you know what you're doing. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. + +-------- + + +**Clipping Illustration:** + +.. image:: fastx_clipper_illustration.png + +**Clipping Example:** + +.. image:: fastx_clipper_example.png + +**In the above example:** + +* Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter). +* Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter). + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_example.png b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_example.png new file mode 100644 index 0000000000000000000000000000000000000000..d04d629d5481ca551d5c7024c34fce28e62b8ef3 GIT binary patch literal 35053 zcmb@tcTiJN*M}Pjp+o4sN$*_(yO!}y(e@K0R;i60Ti&&M0!c+olvBg zP=nL}(%V(v_xtAi^UmBmd$N<6lR2|y?|s%;>sh}QXJnvDMb1VJ005}&=;=HJ00@%* z{H`Y@{xid`*@gdn5jjHdLjiz_B#H}b5CA}~hVg*k~ zNtw0?$awEk-lk=I*Wbx;c&s9HdTB7v?WcYaa-8djn?E091qc(|Ahf3b3ec=J;!XU0 z?9kaEB)!)JAl88c6#%f>x&n-Fixa$5(^5f>+2`$^B?Te&Py+r8P-;dLDfd3?*Y&RU z8!@_j0C?*#K!r;q{ng7Gy-!c+-stD)yw80rV#~s3E0f97`&riDynQX~EZD}7^`J6J 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+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out b/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out new file mode 100644 index 00000000000..9a52a29fe49 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out @@ -0,0 +1,8 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATG ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabb diff --git a/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample b/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample new file mode 100644 index 00000000000..79f88f1c3a7 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample @@ -0,0 +1,13 @@ +# +# Adapter/Linker sequences for FASTX-Clipper tool. +# +# Format: +# Adapter Sequence Descriptive name +# +# Example: +# AAATTTGATAAGATA Our-Adapter +# +# Some adapters can be found here: +# http://seqanswers.com/forums/showthread.php?t=198 +# +#TGTAGGCC Dummy-Adapter (don't use me) diff --git a/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml b/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml new file mode 100644 index 00000000000..e3e7f6f4d81 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Fasta Manipulation +description: Collapse sequences +long_description: | + This tool collapses identical sequences in a FASTA file into a single sequence. +name: fastx_collapser +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml new file mode 100644 index 00000000000..1f5e0a252bf --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -0,0 +1,90 @@ + + sequences + + fastx_toolkit + + + + + + + + + + + + + +**What it does** + +This tool collapses identical sequences in a FASTA file into a single sequence. + +-------- + +**Example** + +Example Input File (Sequence "ATAT" appears multiple times):: + + >CSHL_2_FC0042AGLLOO_1_1_605_414 + TGCG + >CSHL_2_FC0042AGLLOO_1_1_537_759 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_774_520 + TGGC + >CSHL_2_FC0042AGLLOO_1_1_742_502 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_781_514 + TGAG + >CSHL_2_FC0042AGLLOO_1_1_757_487 + TTCA + >CSHL_2_FC0042AGLLOO_1_1_903_769 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_724_499 + ATAT + +Example Output file:: + + >1-1 + TGCG + >2-4 + ATAT + >3-1 + TGGC + >4-1 + TGAG + >5-1 + TTCA + +.. class:: infomark + +Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. + +The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. + +The following output:: + + >2-4 + ATAT + +means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file. + + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta new file mode 100644 index 00000000000..6720c254408 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta @@ -0,0 +1,84 @@ +>1 +TGTATTTACAATGACTAGAAA +>2 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>3 +AGTACAAGGACATGC +>4 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>5 +AGTACAAGGACATGC +>6 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>7 +AGTACAAGGACATGC +>8 +AGTACAAGGACATGC +>9 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>10 +AGTACAAGGACATGC +>11 +AGTACAAGGACATGC +>12 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>13 +CGATTGCCGAAGTCTACCA +>14 +AGTACAAGGACATGC +>15 +CCTTGTAGTGGATTCTGATGA +>16 +AGTACAAGGACATGC +>17 +AGTACAAGGACATGC +>18 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>19 +AGTACAAGGACATGC +>20 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>21 +AGTACAAGGACATGC +>22 +AGTACAAGGACATGC +>23 +CTGCTGCGATCGGTGTGC +>24 +AGTACAAGGACATGC +>25 +ACCATTCGAGCATAC +>26 +AGTACAAGGACATGC +>27 +TCAAATTCTAGATTTTTACGG +>28 +AGTACAAGGACATGC +>29 +TGATTTCCAGAGCCAAT +>30 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>31 +TTACCTCACGATATTGTAATA +>32 +ATGACTTCATCGTCCACCCTTTAGAACT +>33 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>34 +TTCAACGCCGCCGTGAAC +>35 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>36 +CTGCTGCGATCGGTGTGC +>37 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>38 +TTCAACGCCGCCGTGAAC +>39 +TTCAACGCCGCCGTGAAC +>40 +CTGCTGCGATCGGTGTGC +>41 +TTCAACGCCGCCGTGAAC +>42 +TTCAACGCCGCCGTGAAC diff --git a/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out new file mode 100644 index 00000000000..f752ab4d079 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out @@ -0,0 +1,24 @@ +>1-15 +AGTACAAGGACATGC +>2-11 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>3-5 +TTCAACGCCGCCGTGAAC +>4-3 +CTGCTGCGATCGGTGTGC +>5-1 +TCAAATTCTAGATTTTTACGG +>6-1 +ACCATTCGAGCATAC +>7-1 +TGATTTCCAGAGCCAAT +>8-1 +TTACCTCACGATATTGTAATA +>9-1 +TGTATTTACAATGACTAGAAA +>10-1 +CCTTGTAGTGGATTCTGATGA +>11-1 +CGATTGCCGAAGTCTACCA +>12-1 +ATGACTTCATCGTCCACCCTTTAGAACT \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml new file mode 100644 index 00000000000..e7687e1dfc5 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fastq Manipulation +- Graphics +description: Draw nucleotides distribution chart +long_description: | + Creates a stacked-histogram graph for the nucleotide distribution in the FASTQ library. +name: fastx_nucleotides_distribution +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_1.png 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a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml new file mode 100644 index 00000000000..7bb498e9b8b --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -0,0 +1,53 @@ + + + + fastx_toolkit + + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output + + + + + + + + + + +**What it does** + +Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. + +.. class:: infomark + +**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. + +----- + +**Output Examples** + +The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** + +.. image:: fastq_nucleotides_distribution_1.png + +In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** + +.. image:: fastq_nucleotides_distribution_2.png + +The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): + +.. image:: fastq_nucleotides_distribution_3.png + +But most of the time, the chart will look rather random: + +.. image:: fastq_nucleotides_distribution_4.png + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + + diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml b/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml new file mode 100644 index 00000000000..579d1305270 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fastq Manipulation +- Statistics +description: Compute quality statistics +long_description: | + Creates quality statistics report for the given FASTQ library. +name: fastx_quality_statistics +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml new file mode 100644 index 00000000000..17da76c5447 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -0,0 +1,71 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + +**What it does** + +Creates quality statistics report for the given Solexa/FASTQ library. + +.. class:: infomark + +**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools. + +----- + +**The output file will contain the following fields:** + +* column = column number (1 to 36 for a 36-cycles read Solexa file) +* count = number of bases found in this column. +* min = Lowest quality score value found in this column. +* max = Highest quality score value found in this column. +* sum = Sum of quality score values for this column. +* mean = Mean quality score value for this column. +* Q1 = 1st quartile quality score. +* med = Median quality score. +* Q3 = 3rd quartile quality score. +* IQR = Inter-Quartile range (Q3-Q1). +* lW = 'Left-Whisker' value (for boxplotting). +* rW = 'Right-Whisker' value (for boxplotting). +* A_Count = Count of 'A' nucleotides found in this column. +* C_Count = Count of 'C' nucleotides found in this column. +* G_Count = Count of 'G' nucleotides found in this column. +* T_Count = Count of 'T' nucleotides found in this column. +* N_Count = Count of 'N' nucleotides found in this column. + + +For example:: + + 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 + 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 + 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 + 4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0 + 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245 + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq new file mode 100644 index 00000000000..d1bc160aa5d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +BBC?7?B6>ABB?B;BBBCC9&;BCBBBBBBBB>>A +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +8BBB?B;BB8?6@9B8BB=8.&1?,&;931&&&(BB +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +B@.?B=6BBB@.@BBBBBBBBBBBBBBB7=;6(663 +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +B?BBBBBBBBBBBBBBB@6ABBBBB@4@BBBBB77< +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +CBCBBBBBBB6.BBBBBBBBBBB=9&66&1@>6&3& +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +B==2777-BB-0&96866&,66-&.6&66,6-*2.6 +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +BBBBBBBBB9699&9BBBBBA@;BBBBBBBBB9&96 +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +BB<4?A9ABB@>>009.6?@<.6@BBBBBBBBBBBB +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +BBBBBBBB?BBBBBBCCC<,91&6<39;?+6,3,9& diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out new file mode 100644 index 00000000000..852c8122efe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out @@ -0,0 +1,37 @@ +column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count +1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 9 +2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 9 +3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 9 +4 9 17 33 261 29.00 30 33 33 3 26 33 1 2 3 3 0 9 +5 9 22 33 269 29.89 30 33 33 3 26 33 3 3 3 0 0 9 +6 9 22 33 277 30.78 30 33 33 3 26 33 5 3 0 1 0 9 +7 9 21 33 258 28.67 24 33 33 9 21 33 4 1 3 1 0 9 +8 9 12 33 263 29.22 32 33 33 1 31 33 2 1 1 5 0 9 +9 9 29 33 290 32.22 33 33 33 0 33 33 3 3 2 1 0 9 +10 9 23 33 277 30.78 32 33 33 1 31 33 1 4 2 2 0 9 +11 9 12 33 245 27.22 21 31 33 12 12 33 5 2 1 1 0 9 +12 9 13 33 214 23.78 15 24 33 18 13 33 2 4 2 1 0 9 +13 9 5 33 249 27.67 29 31 33 4 23 33 2 1 1 5 0 9 +14 9 5 33 233 25.89 24 33 33 9 11 33 3 3 2 1 0 9 +15 9 15 33 251 27.89 24 33 33 9 15 33 5 1 1 2 0 9 +16 9 23 34 269 29.89 24 33 33 9 23 34 3 1 2 3 0 9 +17 9 13 34 266 29.56 33 33 33 0 33 33 2 3 1 3 0 9 +18 9 21 34 272 30.22 31 33 33 2 28 34 0 5 1 3 0 9 +19 9 5 34 244 27.11 27 30 33 6 18 34 4 4 1 0 0 9 +20 9 11 34 241 26.78 23 32 33 10 11 34 3 4 2 0 0 9 +21 9 13 33 240 26.67 24 27 33 9 13 33 1 4 0 4 0 9 +22 9 5 33 190 21.11 13 21 33 20 5 33 1 4 0 3 1 9 +23 9 5 33 205 22.78 16 26 33 17 5 33 4 4 1 0 0 9 +24 9 5 33 247 27.44 28 31 33 5 21 33 1 5 1 2 0 9 +25 9 11 34 241 26.78 24 33 33 9 11 34 3 4 0 2 0 9 +26 9 5 33 212 23.56 18 31 33 15 5 33 0 6 0 3 0 9 +27 9 5 33 227 25.22 21 26 33 12 5 33 3 4 1 1 0 9 +28 9 21 33 255 28.33 24 31 33 9 21 33 2 4 3 0 0 9 +29 9 5 33 228 25.33 21 30 33 12 5 33 2 4 1 2 0 9 +30 9 10 33 213 23.67 16 28 33 17 10 33 3 4 2 0 0 9 +31 9 5 33 236 26.22 21 31 33 12 5 33 1 4 1 3 0 9 +32 9 5 33 210 23.33 12 29 33 21 5 33 3 3 0 3 0 9 +33 9 5 33 183 20.33 9 21 33 24 5 33 1 4 2 2 0 9 +34 9 5 33 150 16.67 7 17 22 15 5 33 3 4 1 1 0 9 +35 9 13 33 217 24.11 21 24 29 8 13 33 1 4 1 3 0 9 +36 9 5 33 195 21.67 18 21 32 14 5 33 3 2 1 3 0 9 diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml b/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml new file mode 100644 index 00000000000..0412d4c4a27 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Rename sequences +long_description: | + This tool renames the sequence identifiers in a FASTQ/A file. +name: fastx_renamer +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_renamer +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml new file mode 100644 index 00000000000..9db83ac9e8f --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -0,0 +1,70 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool renames the sequence identifiers in a FASTQ/A file. + +.. class:: infomark + +Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc). + +-------- + +**Example** + +The following Solexa-FASTQ file:: + + @CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +CSHL_4_FC042GAMMII_2_1_517_596 + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +Renamed to **nucleotides sequence**:: + + @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +Renamed to **numeric counter**:: + + @1 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +1 + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml b/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml new file mode 100644 index 00000000000..705e0825b16 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Fastq Manipulation +- Fasta Manipulation +description: Reverse-Complement +long_description: | + This tool reverse-complements each sequence in a library. If the + library is a FASTQ, the quality-scores are also reversed. +name: fastx_reverse_complement +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml new file mode 100644 index 00000000000..1dc46aedba9 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -0,0 +1,63 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool reverse-complements each sequence in a library. +If the library is a FASTQ, the quality-scores are also reversed. + +-------- + +**Example** + +Input FASTQ file:: + + @CSHL_1_FC42AGWWWXX:8:1:3:740 + TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA + +CSHL_1_FC42AGWWWXX:8:1:3:740 + 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26 + + +Output FASTQ file:: + + @CSHL_1_FC42AGWWWXX:8:1:3:740 + TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA + +CSHL_1_FC42AGWWWXX:8:1:3:740 + 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33 + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta new file mode 100644 index 00000000000..6767ab70655 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +>CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq new file mode 100644 index 00000000000..c9bb2c58d03 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC ++CSHL__2_FC042NGABCD:8:1:120:202 +40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 +@CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC ++CSHL__2_FC042NGABCD:8:1:103:1185 +40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out new file mode 100644 index 00000000000..0707c85dc3f --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT +>CSHL__2_FC042NGABCD:8:1:103:1185 +GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out new file mode 100644 index 00000000000..65997ea46c2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT ++CSHL__2_FC042NGABCD:8:1:120:202 +8 10 21 -1 10 11 -1 7 3 1 8 40 27 14 40 30 -1 40 20 40 25 40 40 28 40 40 6 40 40 40 40 20 40 40 40 40 +@CSHL__2_FC042NGABCD:8:1:103:1185 +GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT ++CSHL__2_FC042NGABCD:8:1:103:1185 +2 30 25 4 2 8 0 10 3 23 12 22 34 15 36 8 14 17 22 9 0 40 22 30 32 40 40 40 31 33 35 40 40 40 40 40 diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml b/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml new file mode 100644 index 00000000000..fe23448138d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Trim sequences +long_description: | + This tool trims (cut bases from) sequences in a FASTA/Q file. +name: fastx_trimmer +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml new file mode 100644 index 00000000000..d6ebbc502e4 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -0,0 +1,83 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool trims (cut bases from) sequences in a FASTA/Q file. + +-------- + +**Example** + +Input Fasta file (with 36 bases in each sequences):: + + >1-1 + TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC + >2-1 + CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA + + +Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: + + >1-1 + TATGGTCAGAAACCATATGCA + >2-1 + CAGCGAGGCTTTAATGCCATT + +Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences:: + + >1-1 + TCAGA + >2-1 + AGGCT + + ------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta new file mode 100644 index 00000000000..6767ab70655 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +>CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out new file mode 100644 index 00000000000..94f4a66b037 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +TAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +>CSHL__2_FC042NGABCD:8:1:103:1185 +CGATAGATCGGCAGAGCTCGTTTACCGTCTTC diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq new file mode 100644 index 00000000000..c9bb2c58d03 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC ++CSHL__2_FC042NGABCD:8:1:120:202 +40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 +@CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC ++CSHL__2_FC042NGABCD:8:1:103:1185 +40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out new file mode 100644 index 00000000000..bf2127ccfbe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCC ++CSHL__2_FC042NGABCD:8:1:120:202 +40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 +@CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTT ++CSHL__2_FC042NGABCD:8:1:103:1185 +40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 0 9 22 17 14 8 36 15 34 22 12 23 diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + From f84ca38b5b80647af3875741f8cda94efc345b34 Mon Sep 17 00:00:00 2001 From: Dave B Date: Mon, 10 Jul 2017 11:58:45 -0400 Subject: [PATCH 02/35] Upgrade to depend on conda version of fastx. --- .../fasta_clipping_histogram.xml | 7 ++++--- .../fasta_clipping_histogram/fastx_macros.xml | 1 + .../fasta_clipping_histogram/tool_dependencies.xml | 6 ------ .../fastx_toolkit/fasta_formatter/fasta_formatter.xml | 9 +++++---- .../fastx_toolkit/fasta_formatter/fastx_macros.xml | 1 + .../fasta_formatter/tool_dependencies.xml | 6 ------ .../fasta_nucleotide_changer.xml | 9 +++++---- .../fasta_nucleotide_changer/fastx_macros.xml | 1 + .../fasta_nucleotide_changer/tool_dependencies.xml | 6 ------ .../fastq_quality_boxplot/fastq_quality_boxplot.xml | 9 +++++---- .../fastq_quality_boxplot/fastx_macros.xml | 1 + .../fastq_quality_boxplot/tool_dependencies.xml | 6 ------ .../fastq_quality_converter.xml | 9 +++++---- .../fastq_quality_converter/fastx_macros.xml | 1 + .../fastq_quality_converter/tool_dependencies.xml | 6 ------ .../fastq_quality_filter/fastq_quality_filter.xml | 9 +++++---- .../fastq_quality_filter/fastx_macros.xml | 1 + .../fastq_quality_filter/tool_dependencies.xml | 6 ------ .../fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml | 9 +++++---- .../fastx_toolkit/fastq_to_fasta/fastx_macros.xml | 1 + .../fastq_to_fasta/tool_dependencies.xml | 6 ------ .../fastx_artifacts_filter/fastx_artifacts_filter.xml | 9 +++++---- .../fastx_artifacts_filter/fastx_macros.xml | 1 + .../fastx_artifacts_filter/tool_dependencies.xml | 6 ------ .../fastx_barcode_splitter/fastx_barcode_splitter.xml | 9 +++++---- .../fastx_barcode_splitter/fastx_macros.xml | 1 + .../fastx_barcode_splitter/tool_dependencies.xml | 6 ------ .../fastx_toolkit/fastx_clipper/fastx_clipper.xml | 9 +++++---- .../fastx_toolkit/fastx_clipper/fastx_macros.xml | 1 + .../fastx_toolkit/fastx_clipper/tool_dependencies.xml | 6 ------ .../fastx_toolkit/fastx_collapser/fastx_collapser.xml | 9 +++++---- .../fastx_toolkit/fastx_collapser/fastx_macros.xml | 1 + .../fastx_collapser/tool_dependencies.xml | 6 ------ tool_collections/fastx_toolkit/fastx_macros.xml | 11 +++++++++++ .../fastx_nucleotides_distribution/fastx_macros.xml | 1 + .../fastx_nucleotides_distribution.xml | 9 +++++---- .../tool_dependencies.xml | 6 ------ .../fastx_quality_statistics/fastx_macros.xml | 1 + .../fastx_quality_statistics.xml | 9 +++++---- .../fastx_quality_statistics/tool_dependencies.xml | 6 ------ .../fastx_toolkit/fastx_renamer/fastx_macros.xml | 1 + .../fastx_toolkit/fastx_renamer/fastx_renamer.xml | 9 +++++---- .../fastx_toolkit/fastx_renamer/tool_dependencies.xml | 6 ------ .../fastx_reverse_complement/fastx_macros.xml | 1 + .../fastx_reverse_complement.xml | 9 +++++---- .../fastx_reverse_complement/tool_dependencies.xml | 6 ------ .../fastx_toolkit/fastx_trimmer/fastx_macros.xml | 1 + .../fastx_toolkit/fastx_trimmer/fastx_trimmer.xml | 9 +++++---- .../fastx_toolkit/fastx_trimmer/tool_dependencies.xml | 6 ------ 49 files changed, 106 insertions(+), 159 deletions(-) create mode 120000 tool_collections/fastx_toolkit/fasta_clipping_histogram/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fasta_clipping_histogram/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fasta_formatter/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fasta_nucleotide_changer/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastq_quality_boxplot/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastq_quality_boxplot/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastq_quality_converter/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastq_quality_filter/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastq_to_fasta/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_clipper/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_collapser/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml create mode 100644 tool_collections/fastx_toolkit/fastx_macros.xml create mode 120000 tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_renamer/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_trimmer/fastx_macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index 7275e20e31d..68d3879c204 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -1,8 +1,9 @@ chart - - fastx_toolkit - + + fastx_macros.xml + + fasta_clipping_histogram.pl $input $outfile diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fastx_macros.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fastx_macros.xml new file mode 120000 index 00000000000..a6c33dbb713 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml index 52a53ce4426..f5ff4d2bc6a 100644 --- a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml +++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml @@ -1,8 +1,9 @@ - + formatter - - fastx_toolkit - + + fastx_macros.xml + + - + diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml index 5d10921417d..92c6eba82a7 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml @@ -1,11 +1,12 @@ - + + fastx_macros.xml - - fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output - + + fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' + @@ -13,6 +14,12 @@ + + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_stats1.out new file mode 100644 index 00000000000..852c8122efe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_stats1.out @@ -0,0 +1,37 @@ +column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count +1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 9 +2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 9 +3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 9 +4 9 17 33 261 29.00 30 33 33 3 26 33 1 2 3 3 0 9 +5 9 22 33 269 29.89 30 33 33 3 26 33 3 3 3 0 0 9 +6 9 22 33 277 30.78 30 33 33 3 26 33 5 3 0 1 0 9 +7 9 21 33 258 28.67 24 33 33 9 21 33 4 1 3 1 0 9 +8 9 12 33 263 29.22 32 33 33 1 31 33 2 1 1 5 0 9 +9 9 29 33 290 32.22 33 33 33 0 33 33 3 3 2 1 0 9 +10 9 23 33 277 30.78 32 33 33 1 31 33 1 4 2 2 0 9 +11 9 12 33 245 27.22 21 31 33 12 12 33 5 2 1 1 0 9 +12 9 13 33 214 23.78 15 24 33 18 13 33 2 4 2 1 0 9 +13 9 5 33 249 27.67 29 31 33 4 23 33 2 1 1 5 0 9 +14 9 5 33 233 25.89 24 33 33 9 11 33 3 3 2 1 0 9 +15 9 15 33 251 27.89 24 33 33 9 15 33 5 1 1 2 0 9 +16 9 23 34 269 29.89 24 33 33 9 23 34 3 1 2 3 0 9 +17 9 13 34 266 29.56 33 33 33 0 33 33 2 3 1 3 0 9 +18 9 21 34 272 30.22 31 33 33 2 28 34 0 5 1 3 0 9 +19 9 5 34 244 27.11 27 30 33 6 18 34 4 4 1 0 0 9 +20 9 11 34 241 26.78 23 32 33 10 11 34 3 4 2 0 0 9 +21 9 13 33 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zyj8BG{bOw4ue3Gy&nC_P_A(xLV%0xY2Aj983=lhy)&S4TTV&ny9=Olv&JWk`*MWm@ z%Ru&2g8cD4^`Fzr8J7KKEieO4b?dY_-JQ$6!2Vaf`MPz- z_`jY9?v4Mu{NL{Wf4uTv_rJehe`UYD=!XiRWo|&z + (ASCII-Numeric) + fastx_macros.xml - + + fastx_macros.xml - + converter from FASTX-toolkit + fastx_macros.xml - gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v -#if $input.ext == "fastqsanger": --Q 33 -#end if + #if $input.ext == "fastqsanger": + -Q 33 + #end if diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index e0baf042993..b7d55cc96d4 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -1,9 +1,9 @@ - + + fastx_macros.xml - + + fastx_macros.xml - - fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' + + '$__tool_directory__'/fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index ffeea8fb966..493cc0fadd3 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -1,9 +1,9 @@ - + adapter sequences + fastx_macros.xml - + sequences + fastx_macros.xml - - + diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 2ac37359c10..0d1abd22663 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,18 +1,24 @@ - + + + gnuplot + fastx_macros.xml - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output - - + + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out new file mode 100644 index 00000000000..852c8122efe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out @@ -0,0 +1,37 @@ +column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count +1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 9 +2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 9 +3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 9 +4 9 17 33 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z`{O71$2pSqC=-;dQT-cR6sSQ2Kk10&{Wo{>@S>A*(F;c+C=!XNRBJ*GaXTd*=NEp z6yW##Pd-au`3CkF+u^L`{X!(!a;n4c5!r9GgWR9#TAF{_ zQM>xXIM$o6j!%DR6O~Y{7J;&fn(7#I!)TJXCKWI}-nQ778S`e&`I9fds>N+|;_B0O zT_UH+pV6>HG9#jYs|6&WS722Oq5YJ$qJ+lXq!Cu$8!6;tZ!z8z*V_jJFq}eK$MZ}{ zcqM)7_|u{pB?uIXnx%{yjpOzZeJ>UrzGHb61(TPD>K|Zd^*&x&YxIawwe_tcpMV~I q4@_I{$qLNwC9C;iKZR>k))Zpxh%-$(cB>Wy{_Hn2Hb~LKT>U>bt?>u| literal 0 HcmV?d00001 diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index 0b782e4d61c..4feb0f21064 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -1,9 +1,9 @@ - + + fastx_macros.xml - + fastx_macros.xml - - + @@ -26,6 +26,11 @@ zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa b/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa new file mode 100644 index 00000000000..6dd52e0c643 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa @@ -0,0 +1,4 @@ +@CSHL_4_FC042GAMMII_2_1_517_596 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT ++CSHL_4_FC042GAMMII_2_1_517_596 +40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa b/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa new file mode 100644 index 00000000000..2dfe3ffbe82 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa @@ -0,0 +1,4 @@ +@GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT ++GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index d66ab531b3a..9bd448de2ec 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -1,16 +1,16 @@ - + + fastx_macros.xml - - + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index 6e45a9c31b7..7f57d910d10 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -1,16 +1,16 @@ - + + fastx_macros.xml - - + From 89e5bb0345c8a91bd4d619bec17ee760ee2e94ed Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 11:17:53 +0200 Subject: [PATCH 05/35] Explicitly set `-Q` for all non-cs fastq variants -Q 33 is the default, but it needs to be set to -Q 64 for fastqillumina and fastqsolexa. --- .../fasta_nucleotide_changer.xml | 6 +++--- .../fastq_quality_filter/fastq_quality_filter.xml | 15 +++++++++------ .../fastq_to_fasta/fastq_to_fasta.xml | 14 +++++++++----- .../fastx_artifacts_filter.xml | 14 ++++++++------ .../fastx_barcode_splitter.xml | 3 ++- .../fastx_toolkit/fastx_clipper/fastx_clipper.xml | 14 ++++++++------ .../fastx_collapser/fastx_collapser.xml | 14 ++++++++------ .../fastx_quality_statistics.xml | 13 +++++++++---- .../fastx_toolkit/fastx_renamer/fastx_renamer.xml | 14 ++++++++------ .../fastx_reverse_complement.xml | 14 ++++++++------ .../fastx_toolkit/fastx_trimmer/fastx_trimmer.xml | 14 ++++++++------ 11 files changed, 80 insertions(+), 55 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml index d91e168141e..5ad68c35688 100644 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -5,9 +5,9 @@ - + diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index 8552b5d463e..2d4c3d5de60 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -5,12 +5,15 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 82cdfa319d5..7cc953dbc67 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -4,12 +4,16 @@ fastx_macros.xml - gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v - #if $input.ext == "fastqsanger": - -Q 33 - #end if + + - diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index b7d55cc96d4..71a8d638637 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 39c009f2b5d..90ede1f4d1e 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -5,8 +5,9 @@ fastx_macros.xml + '$output' - + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 493cc0fadd3..7f3bff084b9 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 7e2b1015d26..92a3650ee15 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index 4feb0f21064..f78d3491e79 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -5,13 +5,18 @@ fastx_macros.xml - + - + diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index c2e3f537bf9..e24038bd251 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 9bd448de2ec..cc82411a56f 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index 7f57d910d10..cb70824a348 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + From 5f17e09ab5479f0c72f58dfac6ebaaf6732a226f Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 11:30:03 +0200 Subject: [PATCH 06/35] Close command tag --- .../fastx_barcode_splitter/fastx_barcode_splitter.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 90ede1f4d1e..88da87ff900 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -8,6 +8,7 @@ '$output' ]]> + From 02ec6a597b76bc652c54dd95b627f6b32d0abc58 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 12:05:05 +0200 Subject: [PATCH 07/35] Fix command tag ... again --- .../fastx_barcode_splitter/fastx_barcode_splitter.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 88da87ff900..baa28c1a418 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -6,7 +6,7 @@ '$output' + bash "$__tool_directory__"/fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' ]]> From 0c1829714933577fb7582d3ee8e2d61c913d204a Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 12:16:32 +0200 Subject: [PATCH 08/35] Fix requirements --- .../fastx_nucleotides_distribution.xml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 0d1abd22663..c165957397f 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,8 +1,9 @@ - - gnuplot - + + + fastx_macros.xml + fastx_macros.xml From c5a5fc1f5010162841e4652ab3deea851a653ecc Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 12:29:43 +0200 Subject: [PATCH 09/35] Don't fail with gnuplot warnings --- .../fastx_nucleotides_distribution.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index c165957397f..1dedc392a17 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -7,7 +7,7 @@ fastx_macros.xml - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output From 91d043d9826e6fa2dcce7707c5f805047c857046 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 12:38:42 +0200 Subject: [PATCH 10/35] Use simsize comparison for png --- .../fastx_nucleotides_distribution.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 1dedc392a17..c0f0bea65ae 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -17,7 +17,7 @@ - + From 8b6d2af42546a39b5283993d50e09d7b25c0b37a Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 1 Jan 2017 18:40:48 +0100 Subject: [PATCH 11/35] Retab certain fastx tools, remove duplicate macro imports --- .../fasta_clipping_histogram.xml | 4 +-- .../fastq_quality_boxplot.xml | 34 +++++++++---------- .../fastx_nucleotides_distribution.xml | 31 ++++++++--------- 3 files changed, 33 insertions(+), 36 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index be34bf9bd4c..cf14f7fcae1 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -1,9 +1,9 @@ chart + - fastx_macros.xml + fastx_macros.xml - - + fastx_macros.xml - - fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' - - - - - - - - - - - - - - + + fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' + + + + + + + + + + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index c0f0bea65ae..98cfa8506e7 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,25 +1,22 @@ - + fastx_macros.xml - - fastx_macros.xml - - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output - - - - - - - - - - - - + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i '$input' -o '$output' + + + + + + + + + + + + **What it does** From 514e9ea9450ba789e06ebfeb3634bc58156a828d Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 1 Jan 2017 18:47:44 +0100 Subject: [PATCH 12/35] Retab more fastx tools --- .../fastq_to_fasta/fastq_to_fasta.xml | 92 +++++++++---------- .../fastx_clipper/fastx_clipper.xml | 10 +- .../fastx_collapser/fastx_collapser.xml | 10 +- .../fastx_quality_statistics.xml | 10 +- .../fastx_renamer/fastx_renamer.xml | 10 +- .../fastx_reverse_complement.xml | 10 +- .../fastx_trimmer/fastx_trimmer.xml | 10 +- 7 files changed, 76 insertions(+), 76 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 7cc953dbc67..2bd56bd596f 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -1,54 +1,54 @@ - converter from FASTX-toolkit + converter from FASTX-toolkit fastx_macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 7f3bff084b9..2ef9d7f902a 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 92a3650ee15..cdd2f44d704 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index f78d3491e79..2e637de00b1 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index e24038bd251..144d606ff7e 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index cc82411a56f..368a4e2a361 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index cb70824a348..9258f0fa614 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -7,11 +7,11 @@ From 7b47f56b657f5be4f76a24d66f7a58c9db967fa8 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 20 Jan 2017 11:03:08 +0100 Subject: [PATCH 13/35] Replace '.ext ==' pattern with is_of_type --- .../fastq_quality_filter/fastq_quality_filter.xml | 4 ++-- .../fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml | 4 ++-- .../fastx_artifacts_filter/fastx_artifacts_filter.xml | 4 ++-- .../fastx_toolkit/fastx_clipper/fastx_clipper.xml | 4 ++-- .../fastx_toolkit/fastx_collapser/fastx_collapser.xml | 4 ++-- .../fastx_quality_statistics/fastx_quality_statistics.xml | 4 ++-- .../fastx_toolkit/fastx_renamer/fastx_renamer.xml | 4 ++-- .../fastx_reverse_complement/fastx_reverse_complement.xml | 4 ++-- .../fastx_toolkit/fastx_trimmer/fastx_trimmer.xml | 4 ++-- 9 files changed, 18 insertions(+), 18 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index 2d4c3d5de60..f1875adfcb8 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -8,9 +8,9 @@ diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 2bd56bd596f..0af011762ce 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index 71a8d638637..5024af84734 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 2ef9d7f902a..9195a6c3506 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index cdd2f44d704..906e28ec2da 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index 2e637de00b1..3715c39fd2f 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index 144d606ff7e..0382bc61121 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 368a4e2a361..859b7bb3e76 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index 9258f0fa614..2537f5d3b72 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -7,9 +7,9 @@ From 7e2048a6a2ca47a1264ec9151efdd94078fadc5a Mon Sep 17 00:00:00 2001 From: Dave B Date: Wed, 12 Jul 2017 13:49:20 -0400 Subject: [PATCH 14/35] =?UTF-8?q?Merge=20in=20Bj=C3=B6rn's=20changes=20fro?= =?UTF-8?q?m=20galaxyproject/tools-devteam#375,=20update=20wrapper=20versi?= =?UTF-8?q?ons.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../fasta_clipping_histogram/fasta_clipping_histogram.xml | 2 +- .../fastx_toolkit/fasta_formatter/fasta_formatter.xml | 2 +- .../fasta_nucleotide_changer/fasta_nucleotide_changer.xml | 2 +- .../fastq_quality_boxplot/fastq_quality_boxplot.xml | 2 +- .../fastq_quality_converter/fastq_quality_converter.xml | 2 +- .../fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml | 2 +- .../fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml | 2 +- .../fastx_artifacts_filter/fastx_artifacts_filter.xml | 2 +- .../fastx_barcode_splitter/fastx_barcode_splitter.xml | 2 +- tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml | 2 +- .../fastx_toolkit/fastx_collapser/fastx_collapser.xml | 2 +- tool_collections/fastx_toolkit/fastx_macros.xml | 2 +- .../fastx_nucleotides_distribution.xml | 2 +- .../fastx_quality_statistics/fastx_quality_statistics.xml | 2 +- .../fastx_reverse_complement/fastx_reverse_complement.xml | 2 +- tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml | 2 +- 16 files changed, 16 insertions(+), 16 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index cf14f7fcae1..0b39e257dad 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -1,4 +1,4 @@ - + chart diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml index ba11726af28..65289c694ec 100644 --- a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml +++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml @@ -1,9 +1,9 @@ formatter + fastx_macros.xml - + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool re-formats a FASTA file, changing the width of the nucleotides lines. + +**TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line. + +-------- + +**Example** + +Input FASTA file (each nucleotides line is 50 characters long):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC + CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG + TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA + ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG + TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG + aactggtctttacctTTAAGTTG + + +Output FASTA file (with width=80):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT + ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA + ATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC + GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG + +Output FASTA file (with width=0 => single line):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta new file mode 100644 index 00000000000..3c76807ab38 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta @@ -0,0 +1,100 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC +CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG +TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA +GTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTAT +ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATC +TACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT +TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGC +AAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTT +GATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATA +GCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAG +AAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACT +AAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT +TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAA +AGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAG +AGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCA +ACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTC +GCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATA +CATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT +ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATA +ATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG +TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG +GAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAa +ggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaag +ctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatga +taaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt +gtttctctcatggtctgtgagagatatagggtagtcccatatacatcttt +ctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatca +ttttgatgattccagaaccttgcagatgcgagatggtagatgatcaacct +tttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccat +aactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAG +TTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT +GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGC +CAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAA +AAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGA +AGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGT +GTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAA +ATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT +CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATT +AAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGAT +ATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGT +GTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATA +CTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAG +ATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTA +TGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAAT +TTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATT +AGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTT +TTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAAC +GAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT +ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATC +GAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAAT +ACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAG +TTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAA +TCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAA +TGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt +gataatttttttttctttgataatttttttctttttctttaataaatttt +ttggataatttttttttggataaatagttcttttttgataattctaataa +tttttttatttattttttttttttctataattttttttaaaaaatttatt +aatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGAC +AATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATAC +GCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACT +TTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGA +TGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtg +tgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTG +ATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA +ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgt +gcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATT +GCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAA +AAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAA +CGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAG +AGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA +AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAA +GTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtact +atgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgca +tttgaaagataatactaatttacaacttccctaaaaaaggtggggcttga +aaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactt +tagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAA +GTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGT +ACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttat +atCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctc +tcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACT +TGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT +TTGtctctgttcccctctccccccctctctctctctctctctctctctct +ctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTG +TTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTT +AATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAA +CTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTA +CTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA +GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTT +CTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTG +GACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATA +TTA diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out new file mode 100644 index 00000000000..dab0e10a3e3 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out @@ -0,0 +1,10 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out new file mode 100644 index 00000000000..40fbc313e49 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out @@ -0,0 +1,84 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCA +GGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGG +TATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACA +ACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATA +CATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT +TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAA +AAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATT +CTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGG +CACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGC +CTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT +TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGC +ATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTA +AACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCC +ATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGC +TACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT +ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGT +TCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCA +TAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTT +TCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaat +ttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaa +tacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt +gtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatag +tgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaacct +tgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttca +caatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAA +CACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT +GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAG +AAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTG +AAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAA +AACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAA +ATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT +CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATT +TGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACG +GTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAA +ATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTAT +CCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATA +AACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCA +TTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATG +ATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATT +GTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT +ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATG +ATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTG +GTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTT +GGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCT +GCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt +gataatttttttttctttgataatttttttctttttctttaataaattttttggataatt +tttttttggataaatagttcttttttgataattctaataatttttttatttatttttttt +ttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTA +ACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAA +GACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACA +TTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtg +tgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgt +ACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA +ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgt +gagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCAT +GAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGG +AAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGA +GAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA +AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGC +AGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaa +aaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttcc +ctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtc +aaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTT +TGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCT +GTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttctt +gtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAG +TTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT +TTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctct +ttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTT +GCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGT +TGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATT +ATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA +GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTT +AACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGC +TTTGATGCCAATCCAACAATTTTGCATATATTA diff --git a/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml new file mode 100644 index 00000000000..00e61fb218e --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Fasta Manipulation +description: RNA/DNA converter. +long_description: | + This tool converts RNA FASTA files to DNA (and vice-versa). +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fasta_nucleotide_changer +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml new file mode 100644 index 00000000000..e15c606044b --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -0,0 +1,72 @@ + + converter + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool converts RNA FASTA files to DNA (and vice-versa). + +In **RNA-to-DNA** mode, U's are changed into T's. + +In **DNA-to-RNA** mode, T's are changed into U's. + +-------- + +**Example** + +Input RNA FASTA file ( from Sanger's mirBase ):: + + >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 + UGAGGUAGUAGGUUGUAUAGUU + >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 + UCCCUGAGACCUCAAGUGUGA + >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 + UGGAAUGUAAAGAAGUAUGUA + +Output DNA FASTA file (with RNA-to-DNA mode):: + + >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 + TGAGGTAGTAGGTTGTATAGTT + >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 + TCCCTGAGACCTCAAGTGTGA + >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 + TGGAATGTAAAGAAGTATGTA + + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out new file mode 100644 index 00000000000..e46135f36f4 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +UGAGGUAGUAGGUUGUAUAGUU +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +UCCCUGAGACCUCAAGUGUGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +UGGAAUGUAAAGAAGUAUGUA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +UAUCACAGCCAGCUUUGAUGUGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGUGUGGUUAGCUGGUUG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +UCACCGGGUGGAAACUAGCAGU +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +UCACCGGGUGAAAAUUCGCAUG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +UCACCGGGUGAACACUUGCAGU +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +UCACCGGGAGAAAAACUGGAGU +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +UCACCGGGUGUAAAUCAGCUUG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +UCACCGGGUGUACAUCAGCUAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +UCACCGGGUGAAAAAUCACCUA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +UCACCGGGUUAACAUCUACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +UAUCACAGUUUACUUGCUGUCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +UGACUAGAGACACAUUCAGCU +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +UGACUAGAGACACAUUCAGCU +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +UGUCAUGGAGUCGCUCUCUUCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +UGUCAUGGAGGCGCUCUCUUCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +UGAGGUAGGCUCAGUAGAUGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCUGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +UGAUAUGUCUGGUAUUCUUGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +UACCCGUAGCUCCUAUCCAUGUU +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGUACAUAUGUUUCCGUGCU +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGUACAUUUGUUUCCGUGCU +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +UACCCGUAAUCUUCAUAAUCCGAG diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out new file mode 100644 index 00000000000..c42d9dc113f --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +TGAGGTAGTAGGTTGTATAGTT +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +TCCCTGAGACCTCAAGTGTGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +TGGAATGTAAAGAAGTATGTA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +TATCACAGCCAGCTTTGATGTGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGTGTGGTTAGCTGGTTG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +TCACCGGGTGGAAACTAGCAGT +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +TCACCGGGTGAAAATTCGCATG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +TCACCGGGTGAACACTTGCAGT +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +TCACCGGGAGAAAAACTGGAGT +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +TCACCGGGTGTAAATCAGCTTG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +TCACCGGGTGTACATCAGCTAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +TCACCGGGTGAAAAATCACCTA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +TCACCGGGTTAACATCTACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +TATCACAGTTTACTTGCTGTCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +TGACTAGAGACACATTCAGCT +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +TGACTAGAGACACATTCAGCT +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +TGTCATGGAGTCGCTCTCTTCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +TGTCATGGAGGCGCTCTCTTCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +TGAGGTAGGCTCAGTAGATGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCTGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +TGATATGTCTGGTATTCTTGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +TACCCGTAGCTCCTATCCATGTT +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGTACATATGTTTCCGTGCT +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGTACATTTGTTTCCGTGCT +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +TACCCGTAATCTTCATAATCCGAG diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta new file mode 100644 index 00000000000..c42d9dc113f --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +TGAGGTAGTAGGTTGTATAGTT +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +TCCCTGAGACCTCAAGTGTGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +TGGAATGTAAAGAAGTATGTA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +TATCACAGCCAGCTTTGATGTGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGTGTGGTTAGCTGGTTG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +TCACCGGGTGGAAACTAGCAGT +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +TCACCGGGTGAAAATTCGCATG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +TCACCGGGTGAACACTTGCAGT +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +TCACCGGGAGAAAAACTGGAGT +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +TCACCGGGTGTAAATCAGCTTG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +TCACCGGGTGTACATCAGCTAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +TCACCGGGTGAAAAATCACCTA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +TCACCGGGTTAACATCTACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +TATCACAGTTTACTTGCTGTCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +TGACTAGAGACACATTCAGCT +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +TGACTAGAGACACATTCAGCT +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +TGTCATGGAGTCGCTCTCTTCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +TGTCATGGAGGCGCTCTCTTCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +TGAGGTAGGCTCAGTAGATGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCTGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +TGATATGTCTGGTATTCTTGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +TACCCGTAGCTCCTATCCATGTT +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGTACATATGTTTCCGTGCT +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGTACATTTGTTTCCGTGCT +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +TACCCGTAATCTTCATAATCCGAG diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta new file mode 100644 index 00000000000..e46135f36f4 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +UGAGGUAGUAGGUUGUAUAGUU +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +UCCCUGAGACCUCAAGUGUGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +UGGAAUGUAAAGAAGUAUGUA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +UAUCACAGCCAGCUUUGAUGUGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGUGUGGUUAGCUGGUUG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +UCACCGGGUGGAAACUAGCAGU +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +UCACCGGGUGAAAAUUCGCAUG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +UCACCGGGUGAACACUUGCAGU +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +UCACCGGGAGAAAAACUGGAGU +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +UCACCGGGUGUAAAUCAGCUUG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +UCACCGGGUGUACAUCAGCUAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +UCACCGGGUGAAAAAUCACCUA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +UCACCGGGUUAACAUCUACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +UAUCACAGUUUACUUGCUGUCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +UGACUAGAGACACAUUCAGCU +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +UGACUAGAGACACAUUCAGCU +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +UGUCAUGGAGUCGCUCUCUUCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +UGUCAUGGAGGCGCUCUCUUCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +UGAGGUAGGCUCAGUAGAUGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCUGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +UGAUAUGUCUGGUAUUCUUGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +UACCCGUAGCUCCUAUCCAUGUU +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGUACAUAUGUUUCCGUGCU +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGUACAUUUGUUUCCGUGCU +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +UACCCGUAAUCUUCAUAAUCCGAG diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml new file mode 100644 index 00000000000..cd52b7af998 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Fastq Manipulation +- Graphics +- Statistics +description: Draw quality score boxplot +long_description: | + Creates a boxplot graph for the quality scores in the library. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastq_quality_boxplot +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml new file mode 100644 index 00000000000..2c76a645fde --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml @@ -0,0 +1,57 @@ + + + + fastx_toolkit + + fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output + + + + + + + + + + +**What it does** + +Creates a boxplot graph for the quality scores in the library. + +.. class:: infomark + +**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. + +----- + +**Output Examples** + +* Black horizontal lines are medians +* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1) +* Whiskers show outlier at max. 1.5*IQR + + +An excellent quality library (median quality is 40 for almost all 36 cycles): + +.. image:: fastq_quality_boxplot_1.png + + +A relatively good quality library (median quality degrades towards later cycles): + +.. image:: fastq_quality_boxplot_2.png + +A low quality library (median drops quickly): + +.. image:: fastq_quality_boxplot_3.png + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_1.png b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_1.png new file mode 100644 index 0000000000000000000000000000000000000000..f721716a18cf42e5a5e7e534daeeeb17e028bf95 GIT binary patch literal 44508 zcmaI7Wmp?uw8jgC;sjbK?i6<^8iKo|Kyh~{?ry~$3dOBxDNb>3a47EX?!ojs(?rO@+HYoMAC&2fl<`# 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b/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Fastq Manipulation +description: Quality format converter (ASCII-Numeric) +long_description: | + Converts a Solexa FASTQ file to/from numeric or ASCII quality format. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastq_quality_converter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml new file mode 100644 index 00000000000..c143cb89b94 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml @@ -0,0 +1,98 @@ + + (ASCII-Numeric) + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Converts a Solexa FASTQ file to/from numeric or ASCII quality format. + +.. class:: warningmark + +Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). + +----- + +FASTQ with Numeric quality scores:: + + @CSHL__2_FC042AGWWWXX:8:1:120:202 + ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC + +CSHL__2_FC042AGWWWXX:8:1:120:202 + 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 + @CSHL__2_FC042AGWWWXX:8:1:103:1185 + ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC + +CSHL__2_FC042AGWWWXX:8:1:103:1185 + 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 + + +FASTQ with ASCII quality scores:: + + @CSHL__2_FC042AGWWWXX:8:1:120:202 + ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC + +CSHL__2_FC042AGWWWXX:8:1:120:202 + hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH + @CSHL__2_FC042AGWWWXX:8:1:103:1185 + ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC + +CSHL__2_FC042AGWWWXX:8:1:103:1185 + hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq new file mode 100644 index 00000000000..76c0d6c4f2a --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACACACACTCATCGTCGTCCCCCG ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACCC ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out new file mode 100644 index 00000000000..73283203055 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +33 33 34 30 22 30 33 21 29 32 33 33 30 33 26 33 33 33 34 34 24 5 26 33 34 33 33 33 33 33 33 33 33 29 29 32 +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC ++CSHL_3_FC042AGLLWW:1:2:7:33 +23 33 33 33 30 33 26 33 33 23 30 21 31 24 33 23 33 33 28 23 13 5 16 30 11 5 26 24 18 16 5 5 5 7 33 33 +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +33 31 13 30 33 28 21 33 33 33 31 13 31 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 22 28 26 21 7 21 21 18 +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +33 30 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 31 21 32 33 33 33 33 33 31 19 31 33 33 33 33 33 22 22 27 +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACACACACTCATCGTCGTCCCCCG ++CSHL_3_FC042AGLLWW:1:2:7:292 +34 33 34 33 33 33 33 33 33 33 21 13 33 33 33 33 33 33 33 33 33 33 33 28 24 5 21 21 5 16 31 29 21 5 18 5 +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACCC ++CSHL_3_FC042AGLLWW:1:2:7:1819 +33 28 28 17 22 22 22 12 33 33 12 15 5 24 21 23 21 21 5 11 21 21 12 5 13 21 5 21 21 11 21 12 9 17 13 21 +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +33 33 33 33 33 33 33 33 33 24 21 24 24 5 24 33 33 33 33 33 32 31 26 33 33 33 33 33 33 33 33 33 24 5 24 21 +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:8:624 +33 33 27 19 30 32 24 32 33 33 31 29 29 15 15 24 13 21 30 31 27 13 21 31 33 33 33 33 33 33 33 33 33 33 33 33 +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT ++CSHL_3_FC042AGLLWW:1:2:8:250 +33 33 33 33 33 33 33 33 30 33 33 33 33 33 33 34 34 34 27 11 24 16 5 21 27 18 24 26 30 10 21 11 18 11 24 5 diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out new file mode 100644 index 00000000000..76c0d6c4f2a --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACACACACTCATCGTCGTCCCCCG ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACCC ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq new file mode 100644 index 00000000000..e3caaf2d9f2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq @@ -0,0 +1,60 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1601:1525 +40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1713:528 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1236:1157 +40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 +@CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1818:550 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 +@CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC0420AGLLKK:2:1:1764:391 +40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out new file mode 100644 index 00000000000..56cb36d4af0 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out @@ -0,0 +1,60 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +hhhhhhhhhhhhhhhhhh`hhhhPTYIUehhP]Z^ +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +hhhhhhhhhhhhhhhhhhhhhhh;MQ\hhHQ[HMJ +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +hhhhhhhhhhhhhhhDhhZchfhFhh@CZ`[NKZK +@CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1601:1525 +hhhhhhhhhhhhchhLhh^^hhhLdWQXRVYOJbN +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +hhhhhhhhhhhhhhhhhPW\hUhIeMTUGKNNFWJ +@CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1713:528 +hhhhhhhhhhhhhhhhhhhhh`hLfOVTQNLJGVK +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +hhhhhhhhhhhhhhYhhhhhhh_hhKJWhMLQeQV +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +hhhhhhhhhhhhhhhhhhgV_hhL]V@GLHRGCRI +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +hhghhhhhhhhhDhhXbTaUd`h;hMUUZQRYNYU +@CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1236:1157 +hhhhhhhhhhhhhchhhhhahehhhRPTWV_ZJVS +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +hhhhhhhhhhhhhY[hec[hhQh;dKSOSPKLLWK +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +hhhhhhhhhhhhhhhhhhhhhh^hhXRfaZPWVPR +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +hhhhhhhhchghh[ThQbOhhhhO\QDLJJRNCNK +@CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1818:550 +hhhhhhhhhhhhhhd`hahhfeh\][VMTSQQMaR +@CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC0420AGLLKK:2:1:1764:391 +hhhhhhhhhhhahhhhhXhhhhhLhXNIVO]RKhV diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out new file mode 100644 index 00000000000..e3caaf2d9f2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out @@ -0,0 +1,60 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1601:1525 +40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1713:528 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1236:1157 +40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 +@CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1818:550 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 +@CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC0420AGLLKK:2:1:1764:391 +40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml new file mode 100644 index 00000000000..e4cd18d8c65 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Fastq Manipulation +description: Filter by quality +long_description: | + This tool filters reads based on quality scores. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastq_quality_filter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml new file mode 100644 index 00000000000..ba360c7f63c --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -0,0 +1,83 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool filters reads based on quality scores. + +.. class:: infomark + +Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value. + +.. class:: infomark + +Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value. + +-------- + +Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded. + + +**Example**:: + + @CSHL_4_FC042AGOOII:1:2:214:584 + GACAATAAAC + +CSHL_4_FC042AGOOII:1:2:214:584 + 30 30 30 30 30 30 30 30 20 10 + +Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30). + +Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30). + +Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq new file mode 100644 index 00000000000..ea3db077f2e --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +aaaaaaaaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out new file mode 100644 index 00000000000..f274daf1c83 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out @@ -0,0 +1,4 @@ +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out new file mode 100644 index 00000000000..6353aded69b --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml b/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml new file mode 100644 index 00000000000..84f26dfc3e8 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Convert Formats +description: FASTQ to FASTA converter +long_description: | + This tool converts data from FASTQ format to FASTA format. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastq_to_fasta +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml new file mode 100644 index 00000000000..410aa0222b8 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -0,0 +1,82 @@ + + converter from FASTX-toolkit + + fastx_toolkit + + gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v +#if $input.ext == "fastqsanger": +-Q 33 +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool converts data from Solexa format to FASTA format (scroll down for format description). + +-------- + +**Example** + +The following data in Solexa-FASTQ format:: + + @CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +CSHL_4_FC042GAMMII_2_1_517_596 + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +Will be converted to FASTA (with 'rename sequence names' = NO):: + + >CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +Will be converted to FASTA (with 'rename sequence names' = YES):: + + >1 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq new file mode 100644 index 00000000000..d3386dda038 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out new file mode 100644 index 00000000000..c524fd4e12a --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out @@ -0,0 +1,16 @@ +>CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +>CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +>CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT +>CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA +>CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA +>CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +>CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +>CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out new file mode 100644 index 00000000000..c5b35f433d9 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out @@ -0,0 +1,18 @@ +>1 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +>2 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +>3 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +>4 +AATTATTTATTAAATTTTAATAATATGGGAGACACT +>5 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA +>6 +AATTCAAACCACCCCAACCCACACACAGAGATACAA +>7 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +>8 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +>9 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml new file mode 100644 index 00000000000..e0d7e71a27e --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Remove sequencing artifacts +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +long_description: | + This tool filters sequencing artifacts (reads with all but 3 identical bases). +name: fastx_artifacts_filter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml new file mode 100644 index 00000000000..4f7505f5b85 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -0,0 +1,92 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool filters sequencing artifacts (reads with all but 3 identical bases). + +-------- + +**The following is an example of sequences which will be filtered out**:: + + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA + AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA + AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA + AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA + AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta new file mode 100644 index 00000000000..bd848fd4b27 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta @@ -0,0 +1,24 @@ +>CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA +>CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +>CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA +>CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA +>CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +>CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA +>CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out new file mode 100644 index 00000000000..77833e34f4d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out @@ -0,0 +1,14 @@ +>CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA +>CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +>CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +>CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq new file mode 100644 index 00000000000..e3caaf2d9f2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq @@ -0,0 +1,60 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1601:1525 +AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1601:1525 +40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:1713:528 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++CSHL_3_FC0420AGLLKK:2:1:1713:528 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:1236:1157 +AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1236:1157 +40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 +@CSHL_3_FC0420AGLLKK:2:1:1818:550 +AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA ++CSHL_3_FC0420AGLLKK:2:1:1818:550 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 +@CSHL_3_FC0420AGLLKK:2:1:1764:391 +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC0420AGLLKK:2:1:1764:391 +40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out new file mode 100644 index 00000000000..d82412b46e3 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out @@ -0,0 +1,40 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml new file mode 100644 index 00000000000..69416b9584e --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Barcode Splitter +long_description: | + This tool splits a FASTQ file or a regular FASTA file into several files, using barcodes as the split criteria. +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +name: fastx_barcode_splitter +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/barcode_splitter_output_example.png b/tool_collections/fastx_toolkit/fastx_barcode_splitter/barcode_splitter_output_example.png new file mode 100644 index 0000000000000000000000000000000000000000..c0f8944cc8b2d62829943072d36176c3283467a9 GIT binary patch literal 46800 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z;nZ17xdo`ocn;%7YD>7mH6F7nD&w;FKcv^^S*Cj$wA+K3)ofo88;iMD$;R5tc}Kt* zsSaz_D}DAe2b zU(-RV657Gbl4;j^hYm2tINu!h#$E>zj4fyh6Lb69TIWUNoWAE0);FIbcl*WtQvY^g@r>S(02*!;n7l4 z9Qv0M?bQ>%+Gpl1C-&v^45)axG587ToimxhdNvRI{m$4V3tWPrx>yUhH*7{AYz_gaJ+hWVPS z-BeNbKjhzk-mXJ&A^qzh%FK-ZpSye7g!({b%AmcE!`a;jd_J<0N)pxL#=-v&Iu{+a literal 0 HcmV?d00001 diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml new file mode 100644 index 00000000000..3f627f3dffe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -0,0 +1,73 @@ + + + + fastx_toolkit + + fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. + +-------- + +**Barcode file Format** + +Barcode files are simple text files. +Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. +Example:: + + #This line is a comment (starts with a 'number' sign) + BC1 GATCT + BC2 ATCGT + BC3 GTGAT + BC4 TGTCT + +For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). +Sequences matching the barcode will be stored in the appropriate file. + +One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. + +The output of this tool is an HTML file, displaying the split counts and the file locations. + +**Output Example** + +.. image:: barcode_splitter_output_example.png + + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh new file mode 100755 index 00000000000..976404c99aa --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh @@ -0,0 +1,80 @@ +#!/bin/bash + +# FASTX-toolkit - FASTA/FASTQ preprocessing tools. +# Copyright (C) 2009 A. Gordon (gordon@cshl.edu) +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . + +# +#This is a shell script wrapper for 'fastx_barcode_splitter.pl' +# +# 1. Output files are saved at the dataset's files_path directory. +# +# 2. 'fastx_barcode_splitter.pl' outputs a textual table. +# This script turns it into pretty HTML with working URL +# (so lazy users can just click on the URLs and get their files) + +BARCODE_FILE="$1" +FASTQ_FILE="$2" +LIBNAME="$3" +OUTPUT_PATH="$4" +shift 4 +# The rest of the parameters are passed to the split program + +if [ "$OUTPUT_PATH" == "" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 + exit 1 +fi + +#Sanitize library name, make sure we can create a file with this name +LIBNAME=${LIBNAME//\.gz/} +LIBNAME=${LIBNAME//\.txt/} +LIBNAME=${LIBNAME//[^[:alnum:]]/_} + +if [ ! -r "$FASTQ_FILE" ]; then + echo "Error: Input file ($FASTQ_FILE) not found!" >&2 + exit 1 +fi +if [ ! -r "$BARCODE_FILE" ]; then + echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 + exit 1 +fi +mkdir -p "$OUTPUT_PATH" +if [ ! -d "$OUTPUT_PATH" ]; then + echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 + exit 1 +fi + +PUBLICURL="" +BASEPATH="$OUTPUT_PATH/" +#PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" +PREFIX="$BASEPATH""${LIBNAME}__" +SUFFIX=".txt" + +RESULTS=`zcat -f < "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` +if [ $? != 0 ]; then + echo "error" +fi + +# +# Convert the textual tab-separated table into simple HTML table, +# with the local path replaces with a valid URL +echo "" +echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed ' +i
+s|\t||g +a<\/td><\/tr> +' +echo "

" +echo "

" diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq new file mode 100644 index 00000000000..7cbcf9977bd --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq @@ -0,0 +1,168 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out new file mode 100644 index 00000000000..62baea3e96c --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out @@ -0,0 +1,24 @@ + + + + + + + + +

+

+BarcodeCountLocation +
+BC111fastx_barcode_splitter1_fastq__BC1.txt +
+BC212fastx_barcode_splitter1_fastq__BC2.txt +
+BC39fastx_barcode_splitter1_fastq__BC3.txt +
+BC41fastx_barcode_splitter1_fastq__BC4.txt +
+unmatched9fastx_barcode_splitter1_fastq__unmatched.txt +
+total42 +
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt new file mode 100644 index 00000000000..8a7ba617b8d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt @@ -0,0 +1,4 @@ +BC1 GATCT +BC2 ATCGT +BC3 GTGAT +BC4 TGTCT \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml b/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml new file mode 100644 index 00000000000..85d233f0e30 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Clip adapter sequences +long_description: | + This tool clips adapters from the 3''-end of the sequences in a FASTA/FASTQ file. +name: fastx_clipper +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml new file mode 100644 index 00000000000..2fb04f55e49 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -0,0 +1,101 @@ + + adapter sequences + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + use this for hairpin barcoding. keep at 0 unless you know what you're doing. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. + +-------- + + +**Clipping Illustration:** + +.. image:: fastx_clipper_illustration.png + +**Clipping Example:** + +.. image:: fastx_clipper_example.png + +**In the above example:** + +* Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter). +* Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter). + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_example.png b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_example.png new file mode 100644 index 0000000000000000000000000000000000000000..d04d629d5481ca551d5c7024c34fce28e62b8ef3 GIT binary patch literal 35053 zcmb@tcTiJN*M}Pjp+o4sN$*_(yO!}y(e@K0R;i60Ti&&M0!c+olvBg zP=nL}(%V(v_xtAi^UmBmd$N<6lR2|y?|s%;>sh}QXJnvDMb1VJ005}&=;=HJ00@%* z{H`Y@{xid`*@gdn5jjHdLjiz_B#H}b5CA}~hVg*k~ zNtw0?$awEk-lk=I*Wbx;c&s9HdTB7v?WcYaa-8djn?E091qc(|Ahf3b3ec=J;!XU0 z?9kaEB)!)JAl88c6#%f>x&n-Fixa$5(^5f>+2`$^B?Te&Py+r8P-;dLDfd3?*Y&RU z8!@_j0C?*#K!r;q{ng7Gy-!c+-stD)yw80rV#~s3E0f97`&riDynQX~EZD}7^`J6J 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+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out b/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out new file mode 100644 index 00000000000..9a52a29fe49 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out @@ -0,0 +1,8 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATG ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabb diff --git a/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample b/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample new file mode 100644 index 00000000000..79f88f1c3a7 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample @@ -0,0 +1,13 @@ +# +# Adapter/Linker sequences for FASTX-Clipper tool. +# +# Format: +# Adapter Sequence Descriptive name +# +# Example: +# AAATTTGATAAGATA Our-Adapter +# +# Some adapters can be found here: +# http://seqanswers.com/forums/showthread.php?t=198 +# +#TGTAGGCC Dummy-Adapter (don't use me) diff --git a/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml b/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml new file mode 100644 index 00000000000..e3e7f6f4d81 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Fasta Manipulation +description: Collapse sequences +long_description: | + This tool collapses identical sequences in a FASTA file into a single sequence. +name: fastx_collapser +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml new file mode 100644 index 00000000000..1f5e0a252bf --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -0,0 +1,90 @@ + + sequences + + fastx_toolkit + + + + + + + + + + + + + +**What it does** + +This tool collapses identical sequences in a FASTA file into a single sequence. + +-------- + +**Example** + +Example Input File (Sequence "ATAT" appears multiple times):: + + >CSHL_2_FC0042AGLLOO_1_1_605_414 + TGCG + >CSHL_2_FC0042AGLLOO_1_1_537_759 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_774_520 + TGGC + >CSHL_2_FC0042AGLLOO_1_1_742_502 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_781_514 + TGAG + >CSHL_2_FC0042AGLLOO_1_1_757_487 + TTCA + >CSHL_2_FC0042AGLLOO_1_1_903_769 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_724_499 + ATAT + +Example Output file:: + + >1-1 + TGCG + >2-4 + ATAT + >3-1 + TGGC + >4-1 + TGAG + >5-1 + TTCA + +.. class:: infomark + +Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. + +The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. + +The following output:: + + >2-4 + ATAT + +means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file. + + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta new file mode 100644 index 00000000000..6720c254408 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta @@ -0,0 +1,84 @@ +>1 +TGTATTTACAATGACTAGAAA +>2 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>3 +AGTACAAGGACATGC +>4 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>5 +AGTACAAGGACATGC +>6 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>7 +AGTACAAGGACATGC +>8 +AGTACAAGGACATGC +>9 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>10 +AGTACAAGGACATGC +>11 +AGTACAAGGACATGC +>12 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>13 +CGATTGCCGAAGTCTACCA +>14 +AGTACAAGGACATGC +>15 +CCTTGTAGTGGATTCTGATGA +>16 +AGTACAAGGACATGC +>17 +AGTACAAGGACATGC +>18 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>19 +AGTACAAGGACATGC +>20 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>21 +AGTACAAGGACATGC +>22 +AGTACAAGGACATGC +>23 +CTGCTGCGATCGGTGTGC +>24 +AGTACAAGGACATGC +>25 +ACCATTCGAGCATAC +>26 +AGTACAAGGACATGC +>27 +TCAAATTCTAGATTTTTACGG +>28 +AGTACAAGGACATGC +>29 +TGATTTCCAGAGCCAAT +>30 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>31 +TTACCTCACGATATTGTAATA +>32 +ATGACTTCATCGTCCACCCTTTAGAACT +>33 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>34 +TTCAACGCCGCCGTGAAC +>35 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>36 +CTGCTGCGATCGGTGTGC +>37 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>38 +TTCAACGCCGCCGTGAAC +>39 +TTCAACGCCGCCGTGAAC +>40 +CTGCTGCGATCGGTGTGC +>41 +TTCAACGCCGCCGTGAAC +>42 +TTCAACGCCGCCGTGAAC diff --git a/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out new file mode 100644 index 00000000000..f752ab4d079 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out @@ -0,0 +1,24 @@ +>1-15 +AGTACAAGGACATGC +>2-11 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>3-5 +TTCAACGCCGCCGTGAAC +>4-3 +CTGCTGCGATCGGTGTGC +>5-1 +TCAAATTCTAGATTTTTACGG +>6-1 +ACCATTCGAGCATAC +>7-1 +TGATTTCCAGAGCCAAT +>8-1 +TTACCTCACGATATTGTAATA +>9-1 +TGTATTTACAATGACTAGAAA +>10-1 +CCTTGTAGTGGATTCTGATGA +>11-1 +CGATTGCCGAAGTCTACCA +>12-1 +ATGACTTCATCGTCCACCCTTTAGAACT \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml new file mode 100644 index 00000000000..e7687e1dfc5 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fastq Manipulation +- Graphics +description: Draw nucleotides distribution chart +long_description: | + Creates a stacked-histogram graph for the nucleotide distribution in the FASTQ library. +name: fastx_nucleotides_distribution +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_1.png 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a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml new file mode 100644 index 00000000000..7bb498e9b8b --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -0,0 +1,53 @@ + + + + fastx_toolkit + + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output + + + + + + + + + + +**What it does** + +Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. + +.. class:: infomark + +**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. + +----- + +**Output Examples** + +The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** + +.. image:: fastq_nucleotides_distribution_1.png + +In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** + +.. image:: fastq_nucleotides_distribution_2.png + +The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): + +.. image:: fastq_nucleotides_distribution_3.png + +But most of the time, the chart will look rather random: + +.. image:: fastq_nucleotides_distribution_4.png + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + + diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml b/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml new file mode 100644 index 00000000000..579d1305270 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fastq Manipulation +- Statistics +description: Compute quality statistics +long_description: | + Creates quality statistics report for the given FASTQ library. +name: fastx_quality_statistics +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml new file mode 100644 index 00000000000..17da76c5447 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -0,0 +1,71 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + +**What it does** + +Creates quality statistics report for the given Solexa/FASTQ library. + +.. class:: infomark + +**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools. + +----- + +**The output file will contain the following fields:** + +* column = column number (1 to 36 for a 36-cycles read Solexa file) +* count = number of bases found in this column. +* min = Lowest quality score value found in this column. +* max = Highest quality score value found in this column. +* sum = Sum of quality score values for this column. +* mean = Mean quality score value for this column. +* Q1 = 1st quartile quality score. +* med = Median quality score. +* Q3 = 3rd quartile quality score. +* IQR = Inter-Quartile range (Q3-Q1). +* lW = 'Left-Whisker' value (for boxplotting). +* rW = 'Right-Whisker' value (for boxplotting). +* A_Count = Count of 'A' nucleotides found in this column. +* C_Count = Count of 'C' nucleotides found in this column. +* G_Count = Count of 'G' nucleotides found in this column. +* T_Count = Count of 'T' nucleotides found in this column. +* N_Count = Count of 'N' nucleotides found in this column. + + +For example:: + + 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 + 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 + 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 + 4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0 + 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245 + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq new file mode 100644 index 00000000000..d1bc160aa5d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +BBC?7?B6>ABB?B;BBBCC9&;BCBBBBBBBB>>A +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +8BBB?B;BB8?6@9B8BB=8.&1?,&;931&&&(BB +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +B@.?B=6BBB@.@BBBBBBBBBBBBBBB7=;6(663 +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +B?BBBBBBBBBBBBBBB@6ABBBBB@4@BBBBB77< +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +CBCBBBBBBB6.BBBBBBBBBBB=9&66&1@>6&3& +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +B==2777-BB-0&96866&,66-&.6&66,6-*2.6 +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +BBBBBBBBB9699&9BBBBBA@;BBBBBBBBB9&96 +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +BB<4?A9ABB@>>009.6?@<.6@BBBBBBBBBBBB +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +BBBBBBBB?BBBBBBCCC<,91&6<39;?+6,3,9& diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out new file mode 100644 index 00000000000..852c8122efe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out @@ -0,0 +1,37 @@ +column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count +1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 9 +2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 9 +3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 9 +4 9 17 33 261 29.00 30 33 33 3 26 33 1 2 3 3 0 9 +5 9 22 33 269 29.89 30 33 33 3 26 33 3 3 3 0 0 9 +6 9 22 33 277 30.78 30 33 33 3 26 33 5 3 0 1 0 9 +7 9 21 33 258 28.67 24 33 33 9 21 33 4 1 3 1 0 9 +8 9 12 33 263 29.22 32 33 33 1 31 33 2 1 1 5 0 9 +9 9 29 33 290 32.22 33 33 33 0 33 33 3 3 2 1 0 9 +10 9 23 33 277 30.78 32 33 33 1 31 33 1 4 2 2 0 9 +11 9 12 33 245 27.22 21 31 33 12 12 33 5 2 1 1 0 9 +12 9 13 33 214 23.78 15 24 33 18 13 33 2 4 2 1 0 9 +13 9 5 33 249 27.67 29 31 33 4 23 33 2 1 1 5 0 9 +14 9 5 33 233 25.89 24 33 33 9 11 33 3 3 2 1 0 9 +15 9 15 33 251 27.89 24 33 33 9 15 33 5 1 1 2 0 9 +16 9 23 34 269 29.89 24 33 33 9 23 34 3 1 2 3 0 9 +17 9 13 34 266 29.56 33 33 33 0 33 33 2 3 1 3 0 9 +18 9 21 34 272 30.22 31 33 33 2 28 34 0 5 1 3 0 9 +19 9 5 34 244 27.11 27 30 33 6 18 34 4 4 1 0 0 9 +20 9 11 34 241 26.78 23 32 33 10 11 34 3 4 2 0 0 9 +21 9 13 33 240 26.67 24 27 33 9 13 33 1 4 0 4 0 9 +22 9 5 33 190 21.11 13 21 33 20 5 33 1 4 0 3 1 9 +23 9 5 33 205 22.78 16 26 33 17 5 33 4 4 1 0 0 9 +24 9 5 33 247 27.44 28 31 33 5 21 33 1 5 1 2 0 9 +25 9 11 34 241 26.78 24 33 33 9 11 34 3 4 0 2 0 9 +26 9 5 33 212 23.56 18 31 33 15 5 33 0 6 0 3 0 9 +27 9 5 33 227 25.22 21 26 33 12 5 33 3 4 1 1 0 9 +28 9 21 33 255 28.33 24 31 33 9 21 33 2 4 3 0 0 9 +29 9 5 33 228 25.33 21 30 33 12 5 33 2 4 1 2 0 9 +30 9 10 33 213 23.67 16 28 33 17 10 33 3 4 2 0 0 9 +31 9 5 33 236 26.22 21 31 33 12 5 33 1 4 1 3 0 9 +32 9 5 33 210 23.33 12 29 33 21 5 33 3 3 0 3 0 9 +33 9 5 33 183 20.33 9 21 33 24 5 33 1 4 2 2 0 9 +34 9 5 33 150 16.67 7 17 22 15 5 33 3 4 1 1 0 9 +35 9 13 33 217 24.11 21 24 29 8 13 33 1 4 1 3 0 9 +36 9 5 33 195 21.67 18 21 32 14 5 33 3 2 1 3 0 9 diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml b/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml new file mode 100644 index 00000000000..0412d4c4a27 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Rename sequences +long_description: | + This tool renames the sequence identifiers in a FASTQ/A file. +name: fastx_renamer +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_renamer +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml new file mode 100644 index 00000000000..9db83ac9e8f --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -0,0 +1,70 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool renames the sequence identifiers in a FASTQ/A file. + +.. class:: infomark + +Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc). + +-------- + +**Example** + +The following Solexa-FASTQ file:: + + @CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +CSHL_4_FC042GAMMII_2_1_517_596 + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +Renamed to **nucleotides sequence**:: + + @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +Renamed to **numeric counter**:: + + @1 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +1 + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml b/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml new file mode 100644 index 00000000000..705e0825b16 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml @@ -0,0 +1,12 @@ +categories: +- Fastq Manipulation +- Fasta Manipulation +description: Reverse-Complement +long_description: | + This tool reverse-complements each sequence in a library. If the + library is a FASTQ, the quality-scores are also reversed. +name: fastx_reverse_complement +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml new file mode 100644 index 00000000000..1dc46aedba9 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -0,0 +1,63 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool reverse-complements each sequence in a library. +If the library is a FASTQ, the quality-scores are also reversed. + +-------- + +**Example** + +Input FASTQ file:: + + @CSHL_1_FC42AGWWWXX:8:1:3:740 + TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA + +CSHL_1_FC42AGWWWXX:8:1:3:740 + 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26 + + +Output FASTQ file:: + + @CSHL_1_FC42AGWWWXX:8:1:3:740 + TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA + +CSHL_1_FC42AGWWWXX:8:1:3:740 + 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33 + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta new file mode 100644 index 00000000000..6767ab70655 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +>CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq new file mode 100644 index 00000000000..c9bb2c58d03 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC ++CSHL__2_FC042NGABCD:8:1:120:202 +40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 +@CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC ++CSHL__2_FC042NGABCD:8:1:103:1185 +40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out new file mode 100644 index 00000000000..0707c85dc3f --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT +>CSHL__2_FC042NGABCD:8:1:103:1185 +GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out new file mode 100644 index 00000000000..65997ea46c2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT ++CSHL__2_FC042NGABCD:8:1:120:202 +8 10 21 -1 10 11 -1 7 3 1 8 40 27 14 40 30 -1 40 20 40 25 40 40 28 40 40 6 40 40 40 40 20 40 40 40 40 +@CSHL__2_FC042NGABCD:8:1:103:1185 +GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT ++CSHL__2_FC042NGABCD:8:1:103:1185 +2 30 25 4 2 8 0 10 3 23 12 22 34 15 36 8 14 17 22 9 0 40 22 30 32 40 40 40 31 33 35 40 40 40 40 40 diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml b/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml new file mode 100644 index 00000000000..fe23448138d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml @@ -0,0 +1,11 @@ +categories: +- Fasta Manipulation +- Fastq Manipulation +description: Trim sequences +long_description: | + This tool trims (cut bases from) sequences in a FASTA/Q file. +name: fastx_trimmer +owner: devteam +homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer +type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml new file mode 100644 index 00000000000..d6ebbc502e4 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -0,0 +1,83 @@ + + + + fastx_toolkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool trims (cut bases from) sequences in a FASTA/Q file. + +-------- + +**Example** + +Input Fasta file (with 36 bases in each sequences):: + + >1-1 + TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC + >2-1 + CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA + + +Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: + + >1-1 + TATGGTCAGAAACCATATGCA + >2-1 + CAGCGAGGCTTTAATGCCATT + +Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences:: + + >1-1 + TCAGA + >2-1 + AGGCT + + ------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta new file mode 100644 index 00000000000..6767ab70655 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +>CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out new file mode 100644 index 00000000000..94f4a66b037 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out @@ -0,0 +1,4 @@ +>CSHL__2_FC042NGABCD:8:1:120:202 +TAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +>CSHL__2_FC042NGABCD:8:1:103:1185 +CGATAGATCGGCAGAGCTCGTTTACCGTCTTC diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq new file mode 100644 index 00000000000..c9bb2c58d03 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC ++CSHL__2_FC042NGABCD:8:1:120:202 +40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 +@CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC ++CSHL__2_FC042NGABCD:8:1:103:1185 +40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out new file mode 100644 index 00000000000..bf2127ccfbe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out @@ -0,0 +1,8 @@ +@CSHL__2_FC042NGABCD:8:1:120:202 +ACGATAGATCGGAAGAGCTAGTATGCC ++CSHL__2_FC042NGABCD:8:1:120:202 +40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 +@CSHL__2_FC042NGABCD:8:1:103:1185 +ATCACGATAGATCGGCAGAGCTCGTTT ++CSHL__2_FC042NGABCD:8:1:103:1185 +40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 0 9 22 17 14 8 36 15 34 22 12 23 diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml new file mode 100644 index 00000000000..5474ad780d2 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + From 1a458eaf1ad247bf1e10453d7a9a72b245bf325f Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 24 Apr 2018 16:13:11 -0400 Subject: [PATCH 17/35] Condafy, fix tests, update to 0.0.14 --- .../fasta_clipping_histogram.xml | 46 ++++++---- .../fasta_clipping_histogram/macros.xml | 1 + .../test-data/fasta_clipping_histogram-in1.fa | 10 +++ .../test-data/fasta_clipping_histogram-in2.fa | 84 ++++++++++++++++++ .../fasta_clipping_histogram-out1.png | Bin 0 -> 3139 bytes .../fasta_clipping_histogram-out2.png | Bin 0 -> 3058 bytes .../tool_dependencies.xml | 6 -- .../fasta_formatter/fasta_formatter.xml | 12 +-- .../fastx_toolkit/fasta_formatter/macros.xml | 1 + .../fasta_formatter/tool_dependencies.xml | 6 -- .../fasta_nucleotide_changer.xml | 12 +-- .../fasta_nucleotide_changer/macros.xml | 1 + .../tool_dependencies.xml | 6 -- .../fastq_quality_boxplot.xml | 20 +++-- .../fastq_quality_boxplot/macros.xml | 1 + .../test-data/fastq_quality_boxplot-in1.fastq | 37 ++++++++ .../test-data/fastq_quality_boxplot-out1.png | Bin 0 -> 24545 bytes .../tool_dependencies.xml | 6 -- .../fastq_quality_converter.xml | 12 +-- .../fastq_quality_converter/macros.xml | 1 + .../tool_dependencies.xml | 6 -- .../fastq_quality_filter.xml | 12 +-- .../fastq_quality_filter/macros.xml | 1 + .../test-data/fastq_qual_filter1a.out | 32 +++++++ .../test-data/fastq_qual_filter1b.out | 12 +++ .../tool_dependencies.xml | 6 -- .../fastq_to_fasta/fastq_to_fasta.xml | 20 +++-- .../fastx_toolkit/fastq_to_fasta/macros.xml | 1 + .../fastq_to_fasta/tool_dependencies.xml | 6 -- .../fastx_artifacts_filter.xml | 12 +-- .../fastx_artifacts_filter/macros.xml | 1 + .../tool_dependencies.xml | 6 -- .../fastx_barcode_splitter.xml | 12 +-- .../fastx_barcode_splitter/macros.xml | 1 + .../tool_dependencies.xml | 6 -- .../fastx_clipper/fastx_clipper.xml | 12 +-- .../fastx_toolkit/fastx_clipper/macros.xml | 1 + .../fastx_clipper/tool_dependencies.xml | 6 -- .../fastx_collapser/fastx_collapser.xml | 18 ++-- .../fastx_toolkit/fastx_collapser/macros.xml | 1 + .../test-data/fasta_collapser1.out | 14 +-- .../fastx_collapser/tool_dependencies.xml | 6 -- .../fastx_nucleotides_distribution.xml | 25 ++++-- .../fastx_nucleotides_distribution/macros.xml | 1 + .../fastx_nucleotides_distribution-in1.txt | 37 ++++++++ .../fastx_nucleotides_distribution-out1.png | Bin 0 -> 15502 bytes .../tool_dependencies.xml | 6 -- .../fastx_quality_statistics.xml | 12 +-- .../fastx_quality_statistics/macros.xml | 1 + .../tool_dependencies.xml | 6 -- .../fastx_renamer/fastx_renamer.xml | 17 ++-- .../fastx_toolkit/fastx_renamer/macros.xml | 1 + .../test-data/fastx_renamer-in1.fastq | 36 ++++++++ .../test-data/fastx_renamer-out1.fastq | 36 ++++++++ .../fastx_renamer/tool_dependencies.xml | 6 -- .../fastx_reverse_complement.xml | 12 +-- .../fastx_reverse_complement/macros.xml | 1 + .../tool_dependencies.xml | 6 -- .../fastx_trimmer/fastx_trimmer.xml | 12 +-- .../fastx_toolkit/fastx_trimmer/macros.xml | 1 + .../fastx_trimmer/tool_dependencies.xml | 6 -- tool_collections/fastx_toolkit/macros.xml | 21 +++++ 62 files changed, 492 insertions(+), 205 deletions(-) create mode 120000 tool_collections/fastx_toolkit/fasta_clipping_histogram/macros.xml create mode 100644 tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in1.fa create mode 100644 tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in2.fa create mode 100644 tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-out1.png create mode 100644 tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-out2.png delete mode 100644 tool_collections/fastx_toolkit/fasta_clipping_histogram/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fasta_formatter/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fasta_nucleotide_changer/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastq_quality_boxplot/macros.xml create mode 100644 tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-in1.fastq create mode 100644 tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-out1.png delete mode 100644 tool_collections/fastx_toolkit/fastq_quality_boxplot/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastq_quality_converter/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastq_quality_filter/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastq_to_fasta/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_artifacts_filter/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_barcode_splitter/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_clipper/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_collapser/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_nucleotides_distribution/macros.xml create mode 100644 tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-in1.txt create mode 100644 tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-out1.png delete mode 100644 tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_quality_statistics/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_renamer/macros.xml create mode 100644 tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-in1.fastq create mode 100644 tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-out1.fastq delete mode 100644 tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_reverse_complement/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml create mode 120000 tool_collections/fastx_toolkit/fastx_trimmer/macros.xml delete mode 100644 tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml create mode 100644 tool_collections/fastx_toolkit/macros.xml diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index 7275e20e31d..8c887da5070 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -1,9 +1,12 @@ - + chart - - fastx_toolkit - - fasta_clipping_histogram.pl $input $outfile + + macros.xml + + + perl-gdgraph + + fasta_clipping_histogram.pl $input $outfile @@ -13,8 +16,17 @@ + + + + + + + + + sequence1 - AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG - >sequence2 - GTGTGTGTGGGAAGTTGACACAGTA - >sequence3 - CCTTGAGATTAACGCTAATCAAGTAAAC + >sequence1 + AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG + >sequence2 + GTGTGTGTGGGAAGTTGACACAGTA + >sequence3 + CCTTGAGATTAACGCTAATCAAGTAAAC If the sequences span over multiple lines:: - >sequence1 - CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG - TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG - aactggtctttacctTTAAGTTG + >sequence1 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG + TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG + aactggtctttacctTTAAGTTG Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences:: @@ -98,6 +110,8 @@ Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts. This tool is based on `FASTX-toolkit`__ by Assaf Gordon. - .. __: http://hannonlab.cshl.edu/fastx_toolkit/ +.. __: http://hannonlab.cshl.edu/fastx_toolkit/ + ]]> + diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/macros.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in1.fa b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in1.fa new file mode 100644 index 00000000000..dab0e10a3e3 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in1.fa @@ -0,0 +1,10 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 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00000000000..40fbc313e49 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in2.fa @@ -0,0 +1,84 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCA +GGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGG +TATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACA +ACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATA +CATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT +TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAA +AAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATT +CTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGG +CACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGC +CTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT +TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGC +ATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTA +AACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCC 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/dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml index 52a53ce4426..b754b91755b 100644 --- a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml +++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml @@ -1,8 +1,9 @@ - + formatter - - fastx_toolkit - + + macros.xml + + - + @@ -86,4 +87,5 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fasta_formatter/macros.xml b/tool_collections/fastx_toolkit/fasta_formatter/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml index e15c606044b..b00256b40bb 100644 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -1,9 +1,10 @@ - + converter - - fastx_toolkit - - + + macros.xml + + + @@ -69,4 +70,5 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/macros.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml index 2c76a645fde..4eddd4ce35a 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml @@ -1,10 +1,11 @@ - + - - fastx_toolkit - - fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output - + + macros.xml + + + fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output + @@ -12,6 +13,12 @@ + + + + + + **What it does** @@ -53,5 +60,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/macros.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-in1.fastq b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-in1.fastq new file mode 100644 index 00000000000..852c8122efe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-in1.fastq @@ -0,0 +1,37 @@ +column count min 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b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml index c143cb89b94..9d8029c2035 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml @@ -1,9 +1,10 @@ - + (ASCII-Numeric) - - fastx_toolkit - - + + macros.xml + + + @@ -94,5 +95,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/macros.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastq_quality_converter/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index ba360c7f63c..cc02f9046b6 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -1,9 +1,10 @@ - + - - fastx_toolkit - - + + macros.xml + + + + diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/macros.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out index f274daf1c83..ea3db077f2e 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out @@ -1,4 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +aaaaaaaaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out index 6353aded69b..ea3db077f2e 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out @@ -2,6 +2,10 @@ GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +aaaaaaaaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 @@ -14,6 +18,10 @@ a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 @@ -22,3 +30,7 @@ aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 410aa0222b8..0a26b09a835 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -1,9 +1,10 @@ - + converter from FASTX-toolkit - - fastx_toolkit - - gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v + + macros.xml + + + gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v #if $input.ext == "fastqsanger": -Q 33 #end if @@ -24,6 +25,10 @@ + + + + @@ -41,10 +46,6 @@ - - - - **What it does** @@ -78,5 +79,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/macros.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index 4f7505f5b85..2793aa35e7a 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -1,9 +1,10 @@ - + - - fastx_toolkit - - + + macros.xml + + + + diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/macros.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 3f627f3dffe..9bdae3df631 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -1,9 +1,10 @@ - + - - fastx_toolkit - - fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' + + macros.xml + + + bash $__tool_directory__/fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' @@ -69,5 +70,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/macros.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 2fb04f55e49..371d681ebb8 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -1,9 +1,10 @@ - + adapter sequences - - fastx_toolkit - - + + macros.xml + + + + diff --git a/tool_collections/fastx_toolkit/fastx_clipper/macros.xml b/tool_collections/fastx_toolkit/fastx_clipper/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_clipper/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 1f5e0a252bf..c6b37b3bb5f 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -1,9 +1,10 @@ - + sequences - - fastx_toolkit - - + + macros.xml + + + - + - --> **What it does** @@ -87,4 +88,5 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/macros.xml b/tool_collections/fastx_toolkit/fastx_collapser/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out index f752ab4d079..22f9d963491 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out +++ b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out @@ -7,18 +7,18 @@ TTCAACGCCGCCGTGAAC >4-3 CTGCTGCGATCGGTGTGC >5-1 -TCAAATTCTAGATTTTTACGG ->6-1 ACCATTCGAGCATAC +>6-1 +TGTATTTACAATGACTAGAAA >7-1 TGATTTCCAGAGCCAAT >8-1 -TTACCTCACGATATTGTAATA +CGATTGCCGAAGTCTACCA >9-1 -TGTATTTACAATGACTAGAAA +TCAAATTCTAGATTTTTACGG >10-1 -CCTTGTAGTGGATTCTGATGA +TTACCTCACGATATTGTAATA >11-1 -CGATTGCCGAAGTCTACCA +CCTTGTAGTGGATTCTGATGA >12-1 -ATGACTTCATCGTCCACCCTTTAGAACT \ No newline at end of file +ATGACTTCATCGTCCACCCTTTAGAACT diff --git a/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 7bb498e9b8b..616823bf410 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,17 +1,25 @@ - + - - fastx_toolkit - - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output - + + macros.xml + + + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output + - + + + + + + + + **What it does** @@ -29,7 +37,7 @@ Creates a stacked-histogram graph for the nucleotide distribution in the Solexa The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** .. image:: fastq_nucleotides_distribution_1.png - + In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** .. image:: fastq_nucleotides_distribution_2.png @@ -49,5 +57,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/macros.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-in1.txt b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-in1.txt new file mode 100644 index 00000000000..852c8122efe --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-in1.txt @@ -0,0 +1,37 @@ +column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count +1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 9 +2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 9 +3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 9 +4 9 17 33 261 29.00 30 33 33 3 26 33 1 2 3 3 0 9 +5 9 22 33 269 29.89 30 33 33 3 26 33 3 3 3 0 0 9 +6 9 22 33 277 30.78 30 33 33 3 26 33 5 3 0 1 0 9 +7 9 21 33 258 28.67 24 33 33 9 21 33 4 1 3 1 0 9 +8 9 12 33 263 29.22 32 33 33 1 31 33 2 1 1 5 0 9 +9 9 29 33 290 32.22 33 33 33 0 33 33 3 3 2 1 0 9 +10 9 23 33 277 30.78 32 33 33 1 31 33 1 4 2 2 0 9 +11 9 12 33 245 27.22 21 31 33 12 12 33 5 2 1 1 0 9 +12 9 13 33 214 23.78 15 24 33 18 13 33 2 4 2 1 0 9 +13 9 5 33 249 27.67 29 31 33 4 23 33 2 1 1 5 0 9 +14 9 5 33 233 25.89 24 33 33 9 11 33 3 3 2 1 0 9 +15 9 15 33 251 27.89 24 33 33 9 15 33 5 1 1 2 0 9 +16 9 23 34 269 29.89 24 33 33 9 23 34 3 1 2 3 0 9 +17 9 13 34 266 29.56 33 33 33 0 33 33 2 3 1 3 0 9 +18 9 21 34 272 30.22 31 33 33 2 28 34 0 5 1 3 0 9 +19 9 5 34 244 27.11 27 30 33 6 18 34 4 4 1 0 0 9 +20 9 11 34 241 26.78 23 32 33 10 11 34 3 4 2 0 0 9 +21 9 13 33 240 26.67 24 27 33 9 13 33 1 4 0 4 0 9 +22 9 5 33 190 21.11 13 21 33 20 5 33 1 4 0 3 1 9 +23 9 5 33 205 22.78 16 26 33 17 5 33 4 4 1 0 0 9 +24 9 5 33 247 27.44 28 31 33 5 21 33 1 5 1 2 0 9 +25 9 11 34 241 26.78 24 33 33 9 11 34 3 4 0 2 0 9 +26 9 5 33 212 23.56 18 31 33 15 5 33 0 6 0 3 0 9 +27 9 5 33 227 25.22 21 26 33 12 5 33 3 4 1 1 0 9 +28 9 21 33 255 28.33 24 31 33 9 21 33 2 4 3 0 0 9 +29 9 5 33 228 25.33 21 30 33 12 5 33 2 4 1 2 0 9 +30 9 10 33 213 23.67 16 28 33 17 10 33 3 4 2 0 0 9 +31 9 5 33 236 26.22 21 31 33 12 5 33 1 4 1 3 0 9 +32 9 5 33 210 23.33 12 29 33 21 5 33 3 3 0 3 0 9 +33 9 5 33 183 20.33 9 21 33 24 5 33 1 4 2 2 0 9 +34 9 5 33 150 16.67 7 17 22 15 5 33 3 4 1 1 0 9 +35 9 13 33 217 24.11 21 24 29 8 13 33 1 4 1 3 0 9 +36 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HcmV?d00001 diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index 17da76c5447..3cf8aaa04cc 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -1,9 +1,10 @@ - + - - fastx_toolkit - - + + macros.xml + + + @@ -67,5 +68,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/macros.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index 9db83ac9e8f..0167d61c877 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -1,9 +1,10 @@ - + - - fastx_toolkit - - + + macros.xml + + + + + + + + **What it does** @@ -66,5 +72,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + diff --git a/tool_collections/fastx_toolkit/fastx_renamer/macros.xml b/tool_collections/fastx_toolkit/fastx_renamer/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-in1.fastq b/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-in1.fastq new file mode 100644 index 00000000000..d3386dda038 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-in1.fastq @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-out1.fastq b/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-out1.fastq new file mode 100644 index 00000000000..80c7c79e4c0 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-out1.fastq @@ -0,0 +1,36 @@ +@GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@AATTATTTATTAAATTTTAATAATATGGGAGACACT +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++AATTATTTATTAAATTTTAATAATATGGGAGACACT +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@GGAGAAATACACACAATTGGTTAATCCCCCTATATA +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++GGAGAAATACACACAATTGGTTAATCCCCCTATATA +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@AATTCAAACCACCCCAACCCACACACAGAGATACAA +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++AATTCAAACCACCCCAACCCACACACAGAGATACAA +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff --git a/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 1dc46aedba9..1533ff51e76 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -1,9 +1,10 @@ - + - - fastx_toolkit - - + + macros.xml + + + + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/macros.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index d6ebbc502e4..952d32dd106 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -1,9 +1,10 @@ - + - - fastx_toolkit - - + + macros.xml + + + + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/macros.xml b/tool_collections/fastx_toolkit/fastx_trimmer/macros.xml new file mode 120000 index 00000000000..0c6ff6c3756 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/macros.xml @@ -0,0 +1 @@ +../macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml deleted file mode 100644 index 5474ad780d2..00000000000 --- a/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml new file mode 100644 index 00000000000..4592168e4e1 --- /dev/null +++ b/tool_collections/fastx_toolkit/macros.xml @@ -0,0 +1,21 @@ + + + + + fastx_toolkit + + + + + + + @UNPUBLISHED{agordon, + author = "Assaf Gordon", + title = "FASTQ/A short-reads pre-processing tools", + year = "2010", + note = "http://hannonlab.cshl.edu/fastx_toolkit/", + url = "http://hannonlab.cshl.edu/fastx_toolkit/"} + + + + \ No newline at end of file From 3e6b2f7680c7f52cd10f3da0366204c0431f2e95 Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 1 May 2018 10:59:57 -0400 Subject: [PATCH 18/35] Initial incorporation of Lance's enhancements. --- .../fastx_barcode_splitter.xml | 80 +++++++-- .../fastx_barcode_splitter_galaxy_wrapper.sh | 68 +++---- .../test-data/fastx_barcode_splitter1.fastq | 10 +- .../test-data/fastx_barcode_splitter1.out | 31 +--- .../test-data/fastx_barcode_splitter1_BC1.out | 44 +++++ .../test-data/fastx_barcode_splitter1_BC2.out | 48 +++++ .../test-data/fastx_barcode_splitter1_BC3.out | 36 ++++ .../test-data/fastx_barcode_splitter1_BC4.out | 4 + .../fastx_barcode_splitter1_unmatched.out | 36 ++++ .../fastx_barcode_splitter_index.fastq | 168 ++++++++++++++++++ 10 files changed, 445 insertions(+), 80 deletions(-) create mode 100644 tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC1.out create mode 100644 tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC2.out create mode 100644 tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC3.out create mode 100644 tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC4.out create mode 100644 tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_unmatched.out create mode 100644 tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter_index.fastq diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 9bdae3df631..2b06b9182b7 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -4,35 +4,91 @@ macros.xml - bash $__tool_directory__/fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' + '$summary' +]]> + - + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - + - + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh index 976404c99aa..d2108067f8c 100755 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter_galaxy_wrapper.sh @@ -16,65 +16,55 @@ # You should have received a copy of the GNU Affero General Public License # along with this program. If not, see . -# -#This is a shell script wrapper for 'fastx_barcode_splitter.pl' +# Modified by Lance Parsons (lparsons@princeton.edu) +# 2011-03-15 Adapted to allow galaxy to determine filetype +# 2015-10-21 Updated to make compatible with OSX (BSD sed) +# 2015-11-13 Removed LIBRARY_NAME, no longer needed +# 2016-04-28 Output summary as simple tabular output + +# This is a shell script wrapper for 'fastx_barcode_splitter.pl' # # 1. Output files are saved at the dataset's files_path directory. -# -# 2. 'fastx_barcode_splitter.pl' outputs a textual table. -# This script turns it into pretty HTML with working URL -# (so lazy users can just click on the URLs and get their files) + +if [ "$1x" = "x" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2 + exit 1 +fi BARCODE_FILE="$1" FASTQ_FILE="$2" -LIBNAME="$3" -OUTPUT_PATH="$4" +OUTPUT_PATH="$3" +FILETYPE="$4" shift 4 # The rest of the parameters are passed to the split program -if [ "$OUTPUT_PATH" == "" ]; then - echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 - exit 1 +if [ "${OUTPUT_PATH}x" = "x" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2 + exit 1 fi -#Sanitize library name, make sure we can create a file with this name -LIBNAME=${LIBNAME//\.gz/} -LIBNAME=${LIBNAME//\.txt/} -LIBNAME=${LIBNAME//[^[:alnum:]]/_} - if [ ! -r "$FASTQ_FILE" ]; then - echo "Error: Input file ($FASTQ_FILE) not found!" >&2 - exit 1 + echo "Error: Input file ($FASTQ_FILE) not found!" >&2 + exit 1 fi if [ ! -r "$BARCODE_FILE" ]; then - echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 - exit 1 + echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 + exit 1 fi mkdir -p "$OUTPUT_PATH" if [ ! -d "$OUTPUT_PATH" ]; then - echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 - exit 1 + echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 + exit 1 fi -PUBLICURL="" BASEPATH="$OUTPUT_PATH/" -#PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" -PREFIX="$BASEPATH""${LIBNAME}__" -SUFFIX=".txt" +PREFIX="$BASEPATH" +SUFFIX=".$FILETYPE" +DIRECTORY="$(cd "$(dirname "$0")" && pwd)" -RESULTS=`zcat -f < "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` +RESULTS=$(gzip -cdf "$FASTQ_FILE" | "fastx_barcode_splitter.pl" --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@") if [ $? != 0 ]; then - echo "error" + echo "error" fi -# -# Convert the textual tab-separated table into simple HTML table, -# with the local path replaces with a valid URL -echo "" -echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed ' -i
-s|\t||g -a<\/td><\/tr> -' -echo "

" -echo "

" +echo "$RESULTS" \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq index 7cbcf9977bd..f1afc9660d4 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq @@ -158,11 +158,11 @@ aab^V^aU]`aa^aZaa TAGTTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa -@CSHL_3_FC042AGLLWW:1:2:7:203 +@CSHL_3_FC042AGLLWW:1:2:7:203/1 TAGTTTCTCTATGTACA -+CSHL_3_FC042AGLLWW:1:2:7:203 ++CSHL_3_FC042AGLLWW:1:2:7:203/1 aab^V^aU]`aa^aZaa -@CSHL_3_FC042AGLLWW:1:2:7:203 +@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0: TGTCTGAGTATACACAT -+CSHL_3_FC042AGLLWW:1:2:7:203 -aab^V^aU]`aa^aZaa \ No newline at end of file ++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0: +aab^V^aU]`aa^aZaa diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out index 62baea3e96c..bb704378ef5 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out @@ -1,24 +1,7 @@ - - - - - - - - -

-

-BarcodeCountLocation -
-BC111fastx_barcode_splitter1_fastq__BC1.txt -
-BC212fastx_barcode_splitter1_fastq__BC2.txt -
-BC39fastx_barcode_splitter1_fastq__BC3.txt -
-BC41fastx_barcode_splitter1_fastq__BC4.txt -
-unmatched9fastx_barcode_splitter1_fastq__unmatched.txt -
-total42 -
+# Barcode Count +BC1 11 +BC2 12 +BC3 9 +BC4 1 +unmatched 9 +total 42 diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC1.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC1.out new file mode 100644 index 00000000000..e512d0d4ff4 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC1.out @@ -0,0 +1,44 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC2.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC2.out new file mode 100644 index 00000000000..85732c3d098 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC2.out @@ -0,0 +1,48 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC3.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC3.out new file mode 100644 index 00000000000..9780da92424 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC3.out @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC4.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC4.out new file mode 100644 index 00000000000..4ea8151b368 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC4.out @@ -0,0 +1,4 @@ +@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0: +TGTCTGAGTATACACAT ++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0: +aab^V^aU]`aa^aZaa diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_unmatched.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_unmatched.out new file mode 100644 index 00000000000..6dd823f33a8 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_unmatched.out @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203/1 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203/1 +aab^V^aU]`aa^aZaa diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter_index.fastq b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter_index.fastq new file mode 100644 index 00000000000..10adf673908 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter_index.fastq @@ -0,0 +1,168 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTAC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTC ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V +@CSHL_3_FC042AGLLWW:1:2:7:203/2 +TAGTT ++CSHL_3_FC042AGLLWW:1:2:7:203/2 +aab^V +@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0: +TGTCT ++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0: +aab^V From ac9d832578996dd4143476d596b9c64d266b830f Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 1 May 2018 15:12:06 -0400 Subject: [PATCH 19/35] Add test with fastqsanger input. --- .../fastq_to_fasta/fastq_to_fasta.xml | 21 ++++++---- .../test-data/fastq_to_fasta-in2.fastq | 40 +++++++++++++++++++ .../test-data/fastq_to_fasta-out2.out | 20 ++++++++++ 3 files changed, 74 insertions(+), 7 deletions(-) create mode 100644 tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-in2.fastq create mode 100644 tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-out2.out diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 825777fe628..0f107d58bcb 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -39,13 +39,20 @@ - - - - - - - + + + + + + + + + + + + + + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-in2.fastq b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-in2.fastq new file mode 100644 index 00000000000..d82412b46e3 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-in2.fastq @@ -0,0 +1,40 @@ +@CSHL_3_FC0420AGLLKK:2:1:233:1674 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:233:1674 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 +@CSHL_3_FC0420AGLLKK:2:1:136:448 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA ++CSHL_3_FC0420AGLLKK:2:1:136:448 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 +@CSHL_3_FC0420AGLLKK:2:1:237:1037 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:237:1037 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 +@CSHL_3_FC0420AGLLKK:2:1:1805:1464 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1805:1464 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 +@CSHL_3_FC0420AGLLKK:2:1:126:1087 +GAGATATTCGAATGCATCATCAGATGGCACCATCA ++CSHL_3_FC0420AGLLKK:2:1:126:1087 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 +@CSHL_3_FC0420AGLLKK:2:1:1488:1323 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:1488:1323 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 +@CSHL_3_FC0420AGLLKK:2:1:913:199 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:913:199 +40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 +@CSHL_3_FC0420AGLLKK:2:1:928:765 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC ++CSHL_3_FC0420AGLLKK:2:1:928:765 +40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 +@CSHL_3_FC0420AGLLKK:2:1:727:1020 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA ++CSHL_3_FC0420AGLLKK:2:1:727:1020 +40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 +@CSHL_3_FC0420AGLLKK:2:1:758:1799 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC ++CSHL_3_FC0420AGLLKK:2:1:758:1799 +40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-out2.out b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-out2.out new file mode 100644 index 00000000000..abd084d1577 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-out2.out @@ -0,0 +1,20 @@ +>1 +GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +>2 +GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA +>3 +GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +>4 +GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +>5 +GAGATATTCGAATGCATCATCAGATGGCACCATCA +>6 +GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +>7 +GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC +>8 +GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC +>9 +GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +>10 +GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC From 710977275ae370190743c5a3d78c7203438870d6 Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 1 May 2018 15:43:29 -0400 Subject: [PATCH 20/35] Fix linting and tests. --- .../fastx_barcode_splitter.xml | 38 +++++++++---------- 1 file changed, 18 insertions(+), 20 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index daf1f64b26e..f393757d6e3 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -5,12 +5,10 @@ - + @@ -68,13 +66,13 @@ - - - - - - - + + + + + + + @@ -85,14 +83,14 @@ - - - - - - - - + + + + + + + + From 2c726fc468c37811546fb5f2529bf3f15cfe42eb Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 1 May 2018 16:05:29 -0400 Subject: [PATCH 21/35] Remove command that breaks tests. --- .../fastx_barcode_splitter/fastx_barcode_splitter.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index f393757d6e3..1cf307c64c6 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -17,8 +17,7 @@ #else: $refBarcodeLocation.EOL #end if - > '$summary' && - cd - + > '$summary' ]]> From 12ed6a0d57f4127c0e8dcee8ef50fc2cd05f9ae8 Mon Sep 17 00:00:00 2001 From: Dave B Date: Thu, 3 May 2018 14:41:12 -0400 Subject: [PATCH 22/35] Add quotes to input/output files, maybe fix tests. --- .../fasta_clipping_histogram.xml | 6 +++--- .../test-data/histogram.pdf | Bin 3083 -> 0 bytes .../fastq_quality_boxplot.xml | 4 ++-- .../test-data/quality_boxplot_out.png | Bin 23606 -> 0 bytes .../fastq_to_fasta/fastq_to_fasta.xml | 2 +- .../fastx_nucleotides_distribution.xml | 4 ++-- 6 files changed, 8 insertions(+), 8 deletions(-) delete mode 100644 tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/histogram.pdf delete mode 100644 tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/quality_boxplot_out.png diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index 8c887da5070..8476537889b 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -6,7 +6,7 @@ perl-gdgraph - fasta_clipping_histogram.pl $input $outfile + fasta_clipping_histogram.pl '$input' '$outfile' @@ -18,11 +18,11 @@ - + - + diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/histogram.pdf b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/histogram.pdf deleted file mode 100644 index a1ab4acf1e7d00aab8d44028adbffdf00b0228d1..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3083 zcmb7G2~<GVDt7d@XbJ#I&2c=R80%3s*m;|>4m4JOy z%u&BM5J>Im>b<6TznV4(q*~={Z|nV^GX4*)d6UmHFW$5X=eT`o^FzDSjV-Vi-*q#& z=#4u91(U9WY2dN`Hdn+GZQ+sQ?)SX&eSSF_UN8YMn20dmntE3+!@K?@A^73!%k-02 z%YRi8LvjrEk=DB2DYMKj=4##Qde@2Z!X$?+2Px;N?L79>@J^PkPD%Zf7!7$6^$kLP z9RY5jQV`h=zOjbdBk6p%(S)By1&tn65QOjS4uh@_S~WDsYUry%7w#Y+PpeNfFkL!R%#MetL$vX8w>wNTe61b0jWg6 z8EEH0gnR2#JkD=(TCl+=ZI{eapetO|jSG{Dl)a>WZsuJ>TIN|PM}BF5&4FW{b9`0n zl!NnO<6Rm04(_jAsEH0358;1n?I&yPDW0RNkUk=9arG5=Pyr* 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zyj8BG{bOw4ue3Gy&nC_P_A(xLV%0xY2Aj983=lhy)&S4TTV&ny9=Olv&JWk`*MWm@ z%Ru&2g8cD4^`Fzr8J7KKEieO4b?dY_-JQ$6!2Vaf`MPz- z_`jY9?v4Mu{NL{Wf4uTv_rJehe`UYD=!XiRWo|&zmacros.xml - gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v + gunzip -cf '$input' | fastq_to_fasta $SKIPN $RENAMESEQ -o '$output' -v #if $input.ext == "fastqsanger": -Q 33 #else diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 616823bf410..14c54053aad 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -4,7 +4,7 @@ macros.xml - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i '$input' -o '$output' @@ -17,7 +17,7 @@ - + From d002263a6fc4d68203bd44e0474fc426ef5f9643 Mon Sep 17 00:00:00 2001 From: Dave B Date: Thu, 3 May 2018 15:02:51 -0400 Subject: [PATCH 23/35] Fix repository url, bump delta for quality boxplot. --- .../fastx_toolkit/fasta_clipping_histogram/.shed.yml | 2 +- tool_collections/fastx_toolkit/fasta_formatter/.shed.yml | 2 +- .../fastx_toolkit/fasta_nucleotide_changer/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml | 2 +- .../fastq_quality_boxplot/fastq_quality_boxplot.xml | 2 +- .../fastx_toolkit/fastq_quality_converter/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastx_clipper/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastx_collapser/.shed.yml | 2 +- .../fastx_toolkit/fastx_nucleotides_distribution/.shed.yml | 2 +- .../fastx_toolkit/fastx_quality_statistics/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastx_renamer/.shed.yml | 2 +- .../fastx_toolkit/fastx_reverse_complement/.shed.yml | 2 +- tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml | 2 +- 17 files changed, 17 insertions(+), 17 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml index 8838742c67a..e7bf6140bf6 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml @@ -9,5 +9,5 @@ long_description: | homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ name: fasta_clipping_histogram owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram type: unrestricted diff --git a/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml b/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml index 6c1e37fccf3..44f7d5b06de 100644 --- a/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml +++ b/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml @@ -6,5 +6,5 @@ long_description: | This tool re-formats a FASTA file, changing the width of the nucleotides lines. name: fasta_formatter owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_formatter +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter type: unrestricted diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml index 00e61fb218e..f3c636477ef 100644 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml @@ -6,5 +6,5 @@ long_description: | homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ name: fasta_nucleotide_changer owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml index cd52b7af998..f99db138e20 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml @@ -8,5 +8,5 @@ long_description: | homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ name: fastq_quality_boxplot owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml index bf844783f7e..96938abc9f9 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml @@ -16,7 +16,7 @@ - + diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml index 2918e7b321c..791bccfe3c9 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml @@ -6,5 +6,5 @@ long_description: | homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ name: fastq_quality_converter owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml index e4cd18d8c65..ee402e15395 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml @@ -6,5 +6,5 @@ long_description: | homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ name: fastq_quality_filter owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml b/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml index 84f26dfc3e8..09053c5e708 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml @@ -7,5 +7,5 @@ long_description: | homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ name: fastq_to_fasta owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml index e0d7e71a27e..8cbb256861b 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml @@ -7,5 +7,5 @@ long_description: | This tool filters sequencing artifacts (reads with all but 3 identical bases). name: fastx_artifacts_filter owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml index 69416b9584e..adfe8443dab 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml @@ -7,5 +7,5 @@ long_description: | homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ name: fastx_barcode_splitter owner: devteam -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml b/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml index 85d233f0e30..ec81cc34586 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml @@ -7,5 +7,5 @@ long_description: | name: fastx_clipper owner: devteam homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_clipper +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml b/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml index e3e7f6f4d81..1bb65f07db4 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml @@ -6,5 +6,5 @@ long_description: | name: fastx_collapser owner: devteam homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml index e7687e1dfc5..5681a673853 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml @@ -7,5 +7,5 @@ long_description: | name: fastx_nucleotides_distribution owner: devteam homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml b/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml index 579d1305270..3113224771e 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml @@ -7,5 +7,5 @@ long_description: | name: fastx_quality_statistics owner: devteam homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml b/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml index 0412d4c4a27..7ccac40405c 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml @@ -7,5 +7,5 @@ long_description: | name: fastx_renamer owner: devteam homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_renamer +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml b/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml index 705e0825b16..6a9dcbb313d 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml @@ -8,5 +8,5 @@ long_description: | name: fastx_reverse_complement owner: devteam homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement type: unrestricted diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml b/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml index fe23448138d..461bf74566c 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml @@ -7,5 +7,5 @@ long_description: | name: fastx_trimmer owner: devteam homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/ -remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_trimmer +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer type: unrestricted From 3036e0b8137a1ce55c1d863cad3f330d10d8bb2f Mon Sep 17 00:00:00 2001 From: Dave B Date: Fri, 4 May 2018 09:24:13 -0400 Subject: [PATCH 24/35] Unify input parameters, add filetype support. --- .../fasta_clipping_histogram.xml | 2 +- .../fasta_formatter/fasta_formatter.xml | 2 +- .../fasta_nucleotide_changer.xml | 2 +- .../fastq_quality_converter.xml | 10 +++------- .../fastq_quality_filter.xml | 8 ++------ .../fastq_to_fasta/fastq_to_fasta.xml | 13 ++++++------- .../fastx_artifacts_filter.xml | 8 ++------ .../fastx_clipper/fastx_clipper.xml | 8 ++------ .../fastx_collapser/fastx_collapser.xml | 8 ++------ .../fastx_quality_statistics.xml | 5 +++-- .../fastx_renamer/fastx_renamer.xml | 8 ++------ .../fastx_reverse_complement.xml | 8 ++------ .../fastx_trimmer/fastx_trimmer.xml | 8 ++------ tool_collections/fastx_toolkit/macros.xml | 18 ++++++++++++++++++ 14 files changed, 47 insertions(+), 61 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index 8476537889b..3658877906d 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -9,7 +9,7 @@ fasta_clipping_histogram.pl '$input' '$outfile' - + diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml index b754b91755b..0d717c2797b 100644 --- a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml +++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml @@ -19,7 +19,7 @@ zcat -f < '$input' | fasta_formatter -w $width -o '$output' ]]> - + diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml index b00256b40bb..18c38aedde6 100644 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -10,7 +10,7 @@ zcat -f < '$input' | fasta_nucleotide_changer -$mode -v -o '$output' ]]> - + diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml index 9d8029c2035..92e4788672c 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml @@ -6,21 +6,17 @@ - + - - - - - diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index b267e61217f..7c7fee285d3 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -7,16 +7,12 @@ - + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 75be4e83479..bd767556de8 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -4,16 +4,15 @@ macros.xml - gunzip -cf '$input' | fastq_to_fasta $SKIPN $RENAMESEQ -o '$output' -v -#if $input.ext == "fastqsanger": - -Q 33 -#else - -Q 64 -#end if + + - + diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index 3c1b272c915..ff21ccac0f8 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -7,16 +7,12 @@ - + diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 480749ede28..e8de5d83d75 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -7,16 +7,12 @@ - + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 2a775572efa..7dfd8db5520 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -7,16 +7,12 @@ - + diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index 3cf8aaa04cc..fceed713ff0 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -6,12 +6,13 @@ - + diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index c8c8840d116..e1f790bd473 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -7,16 +7,12 @@ - + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 8cd65f6bb72..97d8b0fbd67 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -7,15 +7,11 @@ - + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index 49ed35c29fd..1e61d744d6a 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -7,16 +7,12 @@ - + diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml index 4592168e4e1..98f48d20f56 100644 --- a/tool_collections/fastx_toolkit/macros.xml +++ b/tool_collections/fastx_toolkit/macros.xml @@ -1,5 +1,14 @@ + + + fastx_toolkit @@ -18,4 +27,13 @@ + + + + + + + + + \ No newline at end of file From 9c846dc24c22458740b90059b4cef2bed3f76912 Mon Sep 17 00:00:00 2001 From: Dave B Date: Fri, 4 May 2018 10:04:22 -0400 Subject: [PATCH 25/35] Fix tests for quality converter, add tests for sanger inputs. --- .../fastq_quality_converter.xml | 28 +- .../fastq_quality_converter-in5.fastq | 2000 +++++++++++++++++ .../fastq_quality_converter-in6.fastq | 2000 +++++++++++++++++ .../fastq_quality_converter-out5.fastq | 2000 +++++++++++++++++ .../fastq_quality_converter-out6.fastq | 2000 +++++++++++++++++ 5 files changed, 8018 insertions(+), 10 deletions(-) create mode 100644 tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in5.fastq create mode 100644 tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in6.fastq create mode 100644 tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out5.fastq create mode 100644 tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out6.fastq diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml index 92e4788672c..5a21891033a 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml @@ -24,32 +24,40 @@ zcat -f < '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' - + - - - + + - - + - - - + + - + + + + + + + + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in5.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in5.fastq new file mode 100644 index 00000000000..379f94e2911 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in5.fastq @@ -0,0 +1,2000 @@ +@chr1_177668195_177668687_1:0:0_2:0:0_0/1 +CCCTTGCCTTCCTAGCTTTCAGTATTACCCACTAAGAACACATAAACATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_102240227_102240757_1:0:0_0:0:0_1/1 +AATGGATGCAGAAAATGTGGTACATCTACACAATGGAATCCTACTCAGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_135092709_135093083_1:0:0_0:0:0_2/1 +GATCTTGACATAAAGCAAAGGTTGTTAAACCAAGGCCTGCTTGCCCTGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_173363751_173364238_0:0:0_1:0:0_3/1 +GAGGGCAGAGAGAAAATCTAAAGTGCAGTCTACTGGTCCTCAGTGGAGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_155990043_155990565_1:0:0_0:0:0_4/1 +AAGCTTGCCGGTCTTCTGTGGGGCAGAGAACCCAGCTGCTCTTTTTCTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_3703883_3704401_0:0:0_1:0:0_5/1 +CTCTTGCAGGAATGAAGCCTTAACGAAAATAGACTGGTAGTGACAATATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_148211558_148212105_1:0:0_2:0:0_6/1 +AATTTCTTTAGTGATAATTAGTTTCTTGTATACTTTGCCCTCCTAACCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_30961675_30962138_2:0:0_0:0:0_7/1 +AAAAACAGGAAAACACATCCAAACAGGTAATGGAAATGAACAAAACCATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_86070681_86071151_1:0:0_0:0:0_8/1 +GAGCCACTTGCAGAACATTCTAATTGTTTCCAACTTTAAGAATAATTGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_78259267_78259767_0:0:0_1:0:0_9/1 +TACCTTCACATCCCCCTCTACTTCTTTCCACCCCCGGTCACTGGGATTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_143451378_143451824_2:0:0_1:0:0_a/1 +TCTTTTTGTCTTATAGACGGTGTCTTTTGCCTTGCAGAAACTTTGGAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_163539961_163540475_1:0:0_1:0:0_b/1 +GGCACACCTGTGATCCTGATCTTGAGGCTGGGAGATACAAGTTTCTGACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_70390520_70391012_0:0:0_1:0:0_c/1 +TCAGTTCAACATGTAGAAATCCCTTATGAATAATCTTGTCACTGTCATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_119090463_119090959_0:0:0_0:0:0_d/1 +GATGATGATGATGATGCCCAAGATGATGATGATATAGCATGCCTAAAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_12587911_12588392_1:0:0_2:0:0_e/1 +AGAAACGGCTAGCACATGATTAGTATCCTGTCCTCTCCCATGAGTCTGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_21875665_21876102_0:0:0_1:0:0_f/1 +GCTAAAAGCAGTAAAGAATGAGAACACAGAGTGTTTAATGATATTACGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_22900274_22900767_0:0:0_0:0:0_10/1 +TTCTTTTTTTTTCTTAGAAAATCAGTGTTTACTTATTACTTTTATTAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_97511239_97511754_1:0:0_0:0:0_11/1 +AGAATTTTGGGTCCTGTTTGTGTAGCCAGTCTTTTAGTCTATGTCTTCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_64669865_64670428_2:0:0_2:0:0_12/1 +ACTCACATGATTGAGTTTCTAAAATCCTTACCAGTAATTCCCCCTGGAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_69102786_69103213_3:0:0_1:0:0_13/1 +TTTTCAAAATAGCAAAAACTTTTTTTATTTTTTTGGTGTTCTGCTGCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117742994_117743506_1:0:0_4:0:0_14/1 +CCGGGATCAAGCTCAAGGAGATTGTCCTTGGACCTGACACTATTACTTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_53703453_53703930_0:0:0_1:0:0_15/1 +CGTCACAACATACTGAGCACCAGGAGCAAGTACTGCGGATCTGTGGGACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_17968135_17968661_2:0:0_0:0:0_16/1 +ATCAATAGTACTGTGAAAGCAAATGCTGGTGAGGATGTGAACAAAGGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_126734590_126735074_2:0:0_1:0:0_17/1 +AAGGTCCCCCATACCCACCCCCCAATCCCCTAGCCACCCACTCCCCCTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_15473022_15473574_0:0:0_2:0:0_18/1 +GGGCTCTTCTCTTTGGTGTCATCCTCTGAAGTAGGAACCAGTTCATTAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_32809503_32810008_3:0:0_4:0:0_19/1 +ACACGTGGTGTTCAGTGTCACCCCATGTAGATGGGGATGTTCCCTAGGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_101160086_101160574_0:0:0_2:0:0_1a/1 +TGTGTGTACGACTGTTTCTGTGAAGGTAAACAAGAGGAGGTTGCACATGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_86845143_86845638_2:0:0_0:0:0_1b/1 +AGCCTTAATTAGTAGGGCTTGGTTTTTTTTGGGGGGGTGGGCTTGGGTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_156394447_156394901_0:1:0_1:0:0_1c/1 +TAGGGAACTTTTGGGACAGCATTTGAACTGTAAATAAAGAAAATATCTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_175220096_175220545_0:0:0_1:0:0_1d/1 +GTCAGCATATTCAATCACACTTTACCTCTTCCCTGCCTCACTTCAGTGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_66136304_66136892_1:0:0_0:0:0_1e/1 +CCTTATCACCATCTTTGACCTCTCTTTCCACTGACTGGAACCCCATTTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_56699450_56700040_1:0:0_0:0:0_1f/1 +GTTCAACTCCTGTCTCCCCCACTGCCCCCCCCCCAGCTCAGCCACCTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_60449644_60450153_0:0:0_0:0:0_20/1 +TAGCACCTGTATACAAAAGTCACGTAATGTGGTATGCATGTTTGTTTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_28286517_28287074_0:0:0_0:0:0_21/1 +ATTTTGATTTTCATTTTTTTTCCTGCTTTGAAGTATTGTATAGAGGAATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_127946423_127946897_1:0:0_1:0:0_22/1 +CATTTAATTCCAGCACTCCAGATGCAGAAGCAGGCAGTTTGAGGTCAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_136274524_136275031_0:0:0_3:0:0_23/1 +TAGATTGTGCTTTGATTCAGAGTAAAGAAAAGAGGACATGGCAAAAGCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_122372156_122372666_1:0:0_1:0:0_24/1 +TTGTGTGTGCTCATGTACAAACACACACACACACACTGAAGTTAAAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_19553027_19553520_1:0:0_0:0:0_25/1 +AGATCAAAGATCTGTGAAGAGGGGAACCATGAATACAAATGGTAGAAAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_57071218_57071658_1:0:0_0:0:0_26/1 +CCCTGAGGCATGTGGGCAGCCCTATGTGGACTCCATAGTTGACAAGAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_7557012_7557560_0:0:0_2:1:0_27/1 +TGGCTAAGCCCAACTCCTTACTTACAATTTAGTTATTTGAGCTTCTCTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_18791508_18791966_0:0:0_0:0:0_28/1 +GCATTGGTTGAAAAGCATGAAAGTTCTATGAGGAAAAAAAAAATAGAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_56244256_56244708_0:0:0_0:0:0_29/1 +TCCTTATTGGATTTTATTAAAAACAAAAATGATTATCATGTTTATTTTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_30613322_30613773_2:0:0_1:0:0_2a/1 +GACAGTTTCTATGAACCTCAAACAATAGCACATTTGCATAGCGGGTTCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_161898116_161898586_1:0:0_1:0:0_2b/1 +GTTGATGCTGAGTTATGAGTCCAAATGATGAATGTTGCACTTGAACAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_3742828_3743343_1:0:0_0:0:0_2c/1 +ATAGATGACATAGATACATGATACATGATGTATGATATATACTATATGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_59624032_59624611_1:0:0_0:0:0_2d/1 +ACCTTAGCCATCTAGTTTTTTTGTGATTGTTGTTTGATTTTTGAGATGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_98734890_98735381_1:0:0_2:0:0_2e/1 +AATTGTGACATAGCAGTAACTCTTGTGTCTTAAGTGTGTTGTATCACATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_170863521_170863976_0:0:0_1:0:0_2f/1 +CAGAAACGTCCACTCACTGCTGATGGAGACACAGAACTGCAAGTTTGGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_111611961_111612483_3:0:0_0:0:0_30/1 +TCTTTTTTTATTTTAATATTTATTTATTATTATTAAGTCTAAGTACACTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_125730124_125730581_1:0:0_1:1:0_31/1 +ATTGAAGGGCAATTCCCTTTGCCCTTTATTGCCTCTGCAGGCCATGTGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_10873266_10873801_1:0:0_1:0:0_32/1 +TATAAAGGCAGAGTCTCTCTTTTAACATAAAGCTTTGTCTAGTCAGCTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_175631956_175632547_3:0:0_1:0:0_33/1 +TTTAAGAGAGACTGATGAGATGTGGGAGACGGAAGAGTGTGGAAGGGTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_20372115_20372592_0:0:0_2:0:0_34/1 +TCCTCACTTAAACTATTAGAAGGTAGTCAAATTTTTTTGGAAGAGTATTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_172022589_172023145_0:0:0_2:0:0_35/1 +TACATCATAGTATATGTCATGCTTTTTATGGCTAAGTAATATTCTACTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_168140019_168140474_0:0:0_1:0:0_36/1 +AGAGAGAAAGTGGCAGGGGGTAGACCTGCAGGCCAGGAACATCAAAGGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_12207936_12208461_1:0:0_0:0:0_37/1 +GAATCAAAAAAGAAACTGACATCACAAAAATTCAAAAAAATGTATTGAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_73438005_73438553_2:0:0_0:0:0_38/1 +TTATCATGTTCTTCTCAGGTCCCTCCCCTCTGGCCTCTATCATCCTCCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_152770828_152771350_1:0:0_1:0:0_39/1 +TGGAACAGAATATTTAGACATGTGTATGCTGGGCACAAACCCTTAGGAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_23377131_23377643_1:0:0_1:0:0_3a/1 +TGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCGCGTTAGCTCGGGGGTTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_101774130_101774651_1:0:0_0:0:0_3b/1 +ACCAAAACCAAAACCAAAAACAAACACCTCTGTAATAATCTGTATCTGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44505664_44506178_2:0:0_1:0:0_3c/1 +GTAGAATCACCTGAATATTGAGTTAGGTGATAGAAGAACGAGTTAAAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_136585250_136585783_0:0:0_0:0:0_3d/1 +ACAAGCTGTACCTTAGGACCCCCATGCATTGGCAGTGATTGTGAATAGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_125479421_125479942_1:0:0_1:0:0_3e/1 +CAGTTAGTGATCAACCTCCTGCTGATCAAATTTCCTTGAATGTATGCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_48288718_48289238_0:0:0_2:0:0_3f/1 +GCTGAGAAGAATGTATACCCTTTTGATTTAGGATAAAATGTTCTGTAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_162596088_162596584_0:0:0_1:0:0_40/1 +ATGTTTTATAATTAATGTTTTAAAATTAACTTTACAATACTATGTTTTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_114964476_114965085_0:0:0_0:0:0_41/1 +AAAAATACATTATGGTTTGCAAAGAATATTTAATAATGTTTCTAAAACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_132214583_132215104_0:0:0_1:0:0_42/1 +GAAGGAGAAGGAGAAGGAAAGAAGAAGAAGAAAGTCATCCAGGTCAGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_4422836_4423410_1:0:0_1:0:0_43/1 +TGTAAAGTAGCATAGAACTTGCTTTCTTGTTTTATAGAGATTCTTCGTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72831428_72831958_1:0:0_0:0:0_44/1 +TTGACAAAAGCAACTGAAGGAAGGCAGAGATTATTTTGGCCCTCAGCACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_17626572_17627059_2:0:0_0:0:0_45/1 +TCACACATGAATGCACTCACATATGCACACGTATTTTAAATATAATTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_122621502_122622050_0:0:0_1:0:0_46/1 +CTAAATGTCTTTTATAGTCATTTATTTGGGACTAATCAGATGGATTAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_157981625_157982140_2:0:0_1:0:0_47/1 +AGGGAATTACCGGTTCAGAATTCAAACTTCAAAAGACAGATAAACATTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_86952334_86952916_0:0:0_1:0:0_48/1 +TCTGCAAGTACTCAGCGAAGCTGCCCACACAGGACTTTTCGTCATGTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_56589802_56590323_0:0:0_5:0:0_49/1 +GTCGTGAAGTGACCGACAGTATATATGGCTAAATATATATATATATATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44959275_44959852_2:0:0_0:0:0_4a/1 +CCCGCCGAACTTAGGAAATTAGTCTGACCAGGTGAGAGGTTGCGCCAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_78655270_78655764_0:0:0_1:0:0_4b/1 +GCACAAGGGACTGCCTACTCCTGTTCATGATTTCATGTGGTTGACCCTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_92742731_92743276_3:0:0_1:1:0_4c/1 +TGACCAGGCGGCTGGAGGTCAAGGGTCTGTCGTAAGAGAATCCCATTGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_133350357_133350894_2:0:0_0:0:0_4d/1 +TGGCCAAAAGGACTGGATGATCCAACGTATAGACAGCTGAGGGCGTTAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_18383798_18384307_2:0:0_0:0:0_4e/1 +CTTATTATCCTAATGCTACCAAATCACAAGGTTTGCTGTTTCTTCCTGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_94539200_94539737_1:0:0_1:0:0_4f/1 +CAGTGTTGTTTTTATTTGCATTTCCCTGATGATTAAGGATGTTGAACATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_131360576_131361118_1:1:0_0:0:0_50/1 +CAGGGTGACACAGTGAAACCTTCTCTTAAACAGTTTCCTAGGACATATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_55802170_55802665_0:0:0_1:0:0_51/1 +AATGATATAAAACCATTTGAACTGTTCCTCTTTCGCCCACAACACACACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_160986523_160987031_0:0:0_1:0:0_52/1 +AGCAACAGAGCAACCTTGCAATGGTGGTCGCCAAGGAAACAGCATCATCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_10207724_10208191_1:0:0_1:0:0_53/1 +TCAAGCATCATTCCTTGGGTACAACCCATTTTATTTTTAAATAGGGACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_186877031_186877586_1:0:0_0:0:0_54/1 +TGTGGAACCTATAGGAGCCTTTTCTCAGTCAGTACCACACAGGTGATGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_76761957_76762468_0:0:0_4:0:0_55/1 +ACAAGAGAAAGCTATATCTGGGTCCTTTCAGCGAAATCTTGCTAGTGTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117599116_117599626_3:0:0_1:0:0_56/1 +TGGATGGTTCATTCCTATTTAAAAGAGGGAAACAAATAGTCACTGGAGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_174656805_174657230_0:0:0_2:0:0_57/1 +GCTTATGTTGCTAATGGCCTTGCATCTTCCTCTCAATAATATATGTTTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_31215276_31215715_1:0:0_3:0:0_58/1 +GTGCCTTGTGACTGATTTGGTTTGAAATATTTTTAAGAATAAAATTTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_126165616_126166084_1:0:0_0:0:0_59/1 +TTTTCTTACATCTGAACTTGGGCCAGAAAGCAGTTTAGTTTTCAAAGAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_164029809_164030262_1:0:0_2:0:0_5a/1 +TGTAGGCGGGATGAGCGGAATTCTACCCACACTTCAAATAACCAAAGCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_121717872_121718374_3:0:0_3:0:0_5b/1 +AGTTTGGGACAAGCAGAATAGACATGCAGTTTCCCTTTCCACCACTACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_160410719_160411215_0:0:0_1:0:0_5c/1 +TCTAATTTTTAAGAATGTGTTTATTTTGTGTTTGGGTATGGGATGCTAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_100203985_100204499_0:0:0_1:0:0_5d/1 +GCAAAGAGTAAGATTGCCAACTCTAATTCCCATTTGGCTCCCATGGGCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_177503365_177503816_3:0:0_0:0:0_5e/1 +TAGCTCGATCCAATCACAAACATTTCACGGACACACCAGCAGTCCAGCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_164919242_164919704_1:0:0_1:0:0_5f/1 +CTTTGAAGGTCTGATAGAACTCTGCACTAAATCCATGTGGTCCTGGGCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_36958484_36958940_1:0:0_2:0:0_60/1 +TCTGGAGTTCCACGGGAAATAGACAGCAGCCTGTGTAACGGGGTCCTCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_99520185_99520697_2:0:0_2:0:0_61/1 +GGAGAGGGAGAGGGAGAGGTAGAGGGAGAGGGAGAGGGAGAGGGATAGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_92584393_92584910_1:0:0_1:0:0_62/1 +CCACTCACTCCCACTTCTTGGCCCTGGTGTTCCCCTTTACTGGGGCATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_6665937_6666494_1:0:0_2:0:0_63/1 +GAGGCACAGGTGGGCAGATCTCTGTGAGTTTGAGGCCAGCCTGAAATATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_103781308_103781731_2:0:0_0:0:0_64/1 +CCAATAGTTTTGTCATTGAACTTAAGGCCAACTTAATGGGAAGAAACTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_35981688_35982179_0:0:0_1:0:0_65/1 +TAATAAAGCTTTTTTATTCATGTACACAGGCTACCTCCATAAGGCAGGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_76873892_76874342_1:0:0_1:0:0_66/1 +GGTGTAAACCACCCACCCCTGCCCTTTGCCAGAAACCATCATGTTTATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_148924276_148924708_1:0:0_0:0:0_67/1 +AACACAATGAGCTAGGGGCCCTCCCACATTGTTTCTAATTAAGGCAATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_48352388_48352886_0:0:0_0:0:0_68/1 +TATTTTTCATCCTGAACCTTAATAATCAAGGTGGGGAAGAAACCCTGGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_135109139_135109668_0:0:0_0:0:0_69/1 +GACTAGGAAATAATGCTAGGCACTTGATTGGCCAGCCAGGCTAGAGAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_133271389_133271883_0:0:0_0:0:0_6a/1 +TGGTTTTTTGTTCTATTTTTTTTAAGATTTATTTTATTTATATGAGTACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_143528403_143528953_0:0:0_3:0:0_6b/1 +GAATCCATTGGCTTGATGTTTCTGGTAGCTGATAATCATTACACATGCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_60739061_60739616_3:0:0_1:0:0_6c/1 +GAAGCAAACTTCCCTAACCTAAAGAAATAGATTCCCACAAACATACAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_86239673_86240187_2:0:0_0:0:0_6d/1 +GGTCCTTAGGAGACCCATGCAGTCCCCACTGTACATCGCCAGAAACAGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_8425683_8426176_2:0:0_1:0:0_6e/1 +GTTATTCATCTTGCCATTTTTGAAAATATTAATTATAAGTTTTCTGGTCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_34934564_34935093_3:0:0_0:0:0_6f/1 +CCTTATAAAAAGTAGACATGCCATATAACTACATTTAGATCAGCAGTGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_43897170_43897709_4:0:0_1:0:0_70/1 +TTGTGGGCATGTCCTCTGGACGAATGACAGGCTGTGGGCCTTTCGTACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_64512455_64512956_0:0:0_0:0:0_71/1 +ATTAGAAGGCACAGTATACATGGATGTACATACCCCATGAATAAATACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72637152_72637620_2:0:0_2:0:0_72/1 +TTTTTTTACAAGAAATAAAGCAGGTCGGTTGCTCTTGAGCATGGCAGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_149528405_149528902_2:0:0_0:0:0_73/1 +GCCACTGTTCCCATTGGTTGGGACCCACACGAAGGTCAATCTGCGCATCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_89951120_89951611_2:0:0_1:0:0_74/1 +AGCCTAGCTGGCCCTAAGGGACAGCCCCTCCCATGGCTAGCCAGTCCCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_108291981_108292457_1:0:0_1:0:0_75/1 +GAAAACTTCCCAAACATAAAGAAAGAGATGCGCATGATCATACAAGAAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130354891_130355474_0:1:0_0:0:0_76/1 +ATATCAAGCTCACTCTCTCTTGGCAATGTGCTGGGCACATTCATCACTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_166207187_166207634_1:0:0_3:1:0_77/1 +CAGAGAACCAGCTCAGCTTCTGGCACTCATGTCAGACAGCTTACAACCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_178111549_178112035_3:0:0_3:0:0_78/1 +GTTTTTGAAAAGTGGGTTTTGGGGAATCAACCTCACATCCATGTTCTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_64705135_64705653_1:0:0_3:0:0_79/1 +TGGGATTTGTTTTCTTTTTAGATTTTGCAGACTTGGGTTTATTACTGTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_50237028_50237524_0:0:0_2:0:0_7a/1 +TCATATCCAATATATATAAAGAACTCAAGAAGTTGGACTCTAGAAAACCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_134752385_134752911_2:0:0_0:0:0_7b/1 +TTTCTGGGCCCAAGGTTTTCAGAAAGCAAATCAAATCCTTAGGTGAGCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_168207741_168208312_2:0:0_0:0:0_7c/1 +CCTAGGTAGCCGGCAAATGTGAATGTAATAGAAAATTTAAATTTTAAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_151034392_151034882_0:0:0_0:0:0_7d/1 +GGGGGTAGAACTTTTCCAAATTTTCCAAGAAACTGCCAAATTGATTTCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_149618965_149619431_0:0:0_1:0:0_7e/1 +TTTTTTTTTTTTTTTTTGGAGGGGGTGTTTTTAAAACCCATCAAAAAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72479618_72480144_1:1:0_0:0:0_7f/1 +TGTTCTCTTGAGAGCAAGCAACGTGACGGCTGGTTAGACGGCAGCCGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_18771436_18771929_1:0:0_2:0:0_80/1 +CTTTCGGGATGCAAACCCCTTCAGCTCCTTCAGTCCTTGCTCTAACTCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_177626454_177626877_2:0:0_1:0:0_81/1 +CCAATAGATGTCCATAGTGAAGCCCTCTGTCTCTCTGCACCTCTCTCATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_58671914_58672334_4:0:0_0:0:0_82/1 +GCAGCATTTGGGAGGCAGAGGCATGTGGATCTCTGTGCGATCAAGTACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_123634655_123635138_1:0:0_1:0:0_83/1 +TAGTAAGTTGTATTTTCACCACAGCATGAACCGTTGCTTACAGCATCACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_32777949_32778514_0:0:0_2:0:0_84/1 +AGAACCATTACAATAGTTGAAAGGAGAAAATTTCAGTTAACTAGGGAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_38321026_38321532_2:0:0_2:0:0_85/1 +TTACATGTCTCCTAAATGAGCATACCAGAGTTCGGCCCAGAAGATGCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_31837668_31838221_1:0:0_2:0:0_86/1 +CCTAGAAAAAAGAACAGGCAACTAATAACTACTGAGAGAGGTAGAATTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_189752778_189753180_2:0:0_0:0:0_87/1 +AGGGTCCCACCTCAGGTGGGGACACTGGCATTCCTCATCAAGTCCACCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_43602264_43602720_2:0:0_0:0:0_88/1 +AGCAAACTGGAGATGGTAAAAGGCTGTAACTCTCAAAGCCGATCCCCAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_29558267_29558774_2:0:0_0:0:0_89/1 +TTTTTGATCTTACAGCACAAGCTATTGCTATTATATTCAAGAATTTATCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_59048796_59049203_1:0:0_0:0:0_8a/1 +GTGTACTCTTCAATGTGAGGGTTCCTACTGGAACATGGTCAACCTACAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_31285666_31286194_0:0:0_1:0:0_8b/1 +CAACCAAATTTCACAAACGGAATTATTTAAAATCAAATATATTTAGAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_159055630_159056144_1:0:0_3:0:0_8c/1 +ACAAAACAACTCCAATAGCCATTTTAAAAATCAAACAGTCTAACACGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_163934531_163935036_0:0:0_1:0:0_8d/1 +ACCCTCAGGGAAAGCGTGGCTTTCATCACAGTGTGTGTGAAGCTGTAATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_116610918_116611481_1:0:0_0:0:0_8e/1 +TAAAATCATTTTATTTGGGACTGAGTGTTCTAAAGTTTACCACTCTGAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_141208156_141208756_0:0:0_0:0:0_8f/1 +CTCTTTCAGGGATGGTGCCCAGATATCTAGTGTTCGAACCTGCCTCCTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_45492268_45492792_1:0:0_3:0:0_90/1 +GATCTAAAAATCAAGTATAAACATCAAGGTATAAGTTCTATCTAAAGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_11755179_11755683_0:0:0_1:0:0_91/1 +ATATATGTTGTTGACTTAAAGGCTTTGAGAAACAGAAATTGTAATGGCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_156738022_156738530_2:0:0_2:0:0_92/1 +CTCCAGCCCCTGGACCTTGTGTTATAACACGTGTAAATCATGCCCCCATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_95480426_95480839_0:0:0_0:0:0_93/1 +GAAATGTTTCTGGTATACATGAACATATAAATGCAAAACTTGTTTGCCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_173460574_173461156_3:0:0_1:0:0_94/1 +ACATTTTTGTAAGCACCCATAAAAATGGATATTGTATAGTCTCAGAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_17445381_17445808_2:0:0_4:0:0_95/1 +ACATCGAGACCTTATTTAAGCAAGCCCCCACCCTCCAGAAATCCTTACTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_76540003_76540477_2:0:0_2:0:0_96/1 +GGAGCAACACAATAGAAGACAGAGTTTTCTCTGATACACATTATAGCCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_12896019_12896500_1:0:0_1:0:0_97/1 +TTTTCTTGTAATACTTTAAGGGATTTTTGTGTTTCATCTTTGAGGGCTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_41708628_41709145_0:0:0_1:0:0_98/1 +GGGGAGACAGGAGAATTCTCACAAGTGCCTGGAAGACCTAGCAGCAAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_106826115_106826660_0:0:0_1:0:0_99/1 +TCCTCCTCCTGCTTCTATGAGGGTGTACTCCCACCCACCTACTTCCACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_13247654_13248181_1:0:0_0:0:0_9a/1 +CACAACTCCTCCCAGGTGGGGTGCAGCTCAAGGACGGGTCAGAGGTGTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_117777350_117777861_0:0:0_1:0:0_9b/1 +TCATCTTTTGATACATATGCAGCTAGAGTCAATAGCTCTGAGGTACTGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_77191506_77192008_2:0:0_1:0:0_9c/1 +TTAACACTAAGACAATTAAGCCTCATTTACAAACAAGATTAAAGACATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_36849743_36850269_1:0:0_1:0:0_9d/1 +GATTGATAAGCCCGATCCAATCTAATCAAAAGAGAGACAAAATCTAAATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_148890840_148891366_0:0:0_0:0:0_9e/1 +ATGAAACACTCATCACACTTACTGGATACTTTTGTATACTGTTTGTTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_84671373_84671880_2:0:0_1:0:0_9f/1 +TTCCATATGGATTCTCGGTTGCCTTTCCCTTATCTGTCATCATTTCGTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_102434771_102435253_0:0:0_1:0:0_a0/1 +CTGGATGGGACATTTGTATAACTATTGGATGCTCTCCATAAAATCTATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_100209819_100210321_0:0:0_1:0:0_a1/1 +GCTACTTATTTAATAATTTGTTATTATCTTTAATTATGTGTGTGTGTGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_62044005_62044573_2:0:0_1:0:0_a2/1 +AACATTTTAAATGCGCAACCTAAGAGGCAGCATGGGCCATGGGGCAGAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_85132332_85132871_1:0:0_3:0:0_a3/1 +AAAGTCCCACACAATAGTGACATGGCTGCAGTTAGGGAAAATGGAACATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_58843215_58843696_0:0:0_0:0:0_a4/1 +AGCCAGGGCTACACAGAGAAACCCTGTCTTGAAAAAAAAAAAAAAGATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_137975188_137975732_1:0:0_1:1:0_a5/1 +TCTTTTATATAATACACCCTGACCACAGATTTCCTTCCCTCTCTACCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_141967561_141968074_0:0:0_0:0:0_a6/1 +ACCACAATATGAAGAACTGTTTTAAAAAGTTGCAGAATTAGGAAGGTTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_8624607_8625140_1:0:0_1:0:0_a7/1 +AAGAAAACCATAGTTTAGTTCTGTGGATGTGGCTGAGAGGTTCACCATGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_138783244_138783650_1:0:0_1:0:0_a8/1 +GGCAAATAACTACATGAGATGCAATTTCCCAAGTTCCCTCTCTCTTCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_52699200_52699639_1:0:0_1:0:0_a9/1 +AAGATATGGGCACAGGGGAAAAATTACTGAATAGAACAGCAAAGGCTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_32849205_32849709_0:0:0_0:0:0_aa/1 +AGTGGATGATCACAGTCAACTATTGGATGGATCACACGGCCCCCATGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_182043596_182044137_0:0:0_0:0:0_ab/1 +CAACCATCTGTACAGCTACAGTGTGCTCATACACATAAAATACATAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_136004325_136004842_4:0:0_0:0:0_ac/1 +TAGTCTACATAGAGAGCTCCAGGACAGGCCGAGCTACAAATTGAGAGCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_174545541_174546018_2:0:0_1:0:0_ad/1 +CGCCCCATTGTGCATTCGATCTCCCCAAGTGTTTTCATTATTACATGATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_11117502_11117925_0:0:0_1:0:0_ae/1 +CCATCCACTAAAAGTTACAGAACTTAGCTGGCACAATGGACAGAATGTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_44177515_44177974_0:0:0_3:0:0_af/1 +ATAATGATCTCTTCATCAGAGGAGCATTAAAAGAAAAAAGAAAGTGTGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_72645507_72646002_0:0:0_0:0:0_b0/1 +GCGCCTAGATTGGGCAGATCTACCACTACACTACCATCTTCCACATCTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_147283777_147284272_0:0:0_1:0:0_b1/1 +TCATACAAGAAGCATACAGAACTCCAAATAGACTGGACCAGAAAAGAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_133675964_133676447_1:0:0_0:0:0_b2/1 +ATCACACAGGCTCTTCCCTAAATATTTCTTCATTATTGCGGTGGTTTCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_114568587_114569130_0:0:0_0:0:0_b3/1 +TTTCAATATTTTTTAGATGACCTATGAATGAATAACTAGGAATTTTGTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_111695385_111695895_0:0:0_0:0:0_b4/1 +TAGCCCCTTAGCTGACCTCTGGCTTTTCACCCTTGCTGTTACTGCAAGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_172273320_172273788_1:0:0_0:0:0_b5/1 +GTCCTCTCTGTCCATAAGGCTCAGGAGTCACAGAAGGTCCAGCTATCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_29014340_29014871_0:0:0_2:0:0_b6/1 +GCCACTCATTTACATCAAATAAATCCCCTGTATTCCAAGGCACCGTATTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_177626521_177627066_1:1:0_0:0:0_b7/1 +CCGTGTGTGTTTCTCTGTGTCTCTCTTTCTTTGTATGTATGCTTCTCTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_110742845_110743354_1:0:0_0:0:0_b8/1 +AATGGGTACAGAAAATGTGATACATTTGCACACTGGAATCCTACTCAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_14101155_14101687_3:0:0_0:0:0_b9/1 +ATACAAACAGAGGTCAATGTCAAACTTCAGCCTCCTTTCTTTCCAGATGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_38147934_38148475_0:0:0_0:0:0_ba/1 +TCTCCCCCACCTCTCACATATACATACATGAGTGTAATTCTTAAACATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_84834550_84834957_2:0:0_1:0:0_bb/1 +TATTTGCACAGGTAGTTAATTTTTGAAACAGGGTGTCATGTAACCCGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_94046734_94047311_0:2:0_1:0:0_bc/1 +AAAGTCAGGCTGGTCTGTTGATTTTTACAAATGAAAGGAGTGTCTGTGCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_138724568_138725155_1:0:0_2:0:0_bd/1 +TAACATATATATTAATGTTCTTATCCAGAGAACACAAAATAGTGAATTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_105672406_105672966_0:0:0_1:0:0_be/1 +TGGTGGCACACGCCTTTAATCCGAGCACTCCGGAGGCAGAGGCAGGCGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_157814995_157815529_0:0:0_3:0:0_bf/1 +TTCCCATTCTCCAGCTCCACCCTAAAATACCACGTCGCTGACTACAGCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_130059190_130059641_1:0:0_0:0:0_c0/1 +CAGTGCTTCCTCCAATTCTAACATAAGAGTCTCTGACCTGTGACCAATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_18604367_18604942_1:0:0_0:0:0_c1/1 +GAACTGAAGCATGGACCTTTGCTGGATTACTCTCTATGTCTTGCTTGGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_160029930_160030407_0:0:0_1:0:0_c2/1 +GCTTGTTTCCTTATCGAAGCCAAGACTACCAGCCCAGGCATGGAACCACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_32417120_32417575_0:0:0_3:0:0_c3/1 +AAATAGCCATGTTACTTTTTAAAGAAGAAACTTGACAGGCTCTAGATTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_91572336_91572825_0:0:0_3:0:0_c4/1 +TTGAGTCATCACATACTGCTGACAAGGAGGCCGTCAAGCCGGTCCACACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_167308006_167308522_0:0:0_0:0:0_c5/1 +CGTGTCCGTCCCCCCCCAACCCCCCGGCTGTTTTTTTTTTTCTTTCTTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_53658226_53658697_1:0:0_1:0:0_c6/1 +AATCAAAACAACCCTGAGATTCCATCTCACACCAGTCCGAATGGCTAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_75542501_75543075_2:0:0_0:0:0_c7/1 +AGTAATCTACAGCAGAAACAGAAAGGGTGGAGATGACCCAGCATCTGGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_49392954_49393517_0:0:0_2:0:0_c8/1 +AGTGCTCTCTAAAGTTTTTGCCTCTCAGTAGAATCCATTCCCAACATGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_18890524_18891056_1:0:0_0:0:0_c9/1 +AACAATCCTGAAGTGCCTGTGCCATCACGAGCAGGGACATAGTAATCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_13661516_13661931_1:0:0_1:0:0_ca/1 +GTGCGCCACCACCACCCGGCAGTTCTTAACTCTTAACAGGCCCAATTTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_69507936_69508419_2:0:0_1:0:0_cb/1 +AATCTTATAGTGTATGGAATATACATCAAATGACAAATCAGATTCCCTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_171186227_171186672_2:0:0_1:0:0_cc/1 +TTCCCGTTCTGGAAAAGAAGAGACCCCTGCCCCCTGCCCCTTCCTGCCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_151167139_151167658_0:0:0_3:0:0_cd/1 +AGAGACAAGTCTTGGCTAAGGGAAGCAAAGTGAGAGATTGGGTTCAGCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_166490443_166490901_1:0:0_2:0:0_ce/1 +CTTCCTGTCCACATCAATAAGCCGCCATTCTGTGGGCTGCCGACTGACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_78053476_78053981_1:0:0_0:0:0_cf/1 +ATAAAACTTGAACTTCATAAAATTCAGATGTCTAGAAGACAGAGACAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_27573317_27573793_0:0:0_2:0:0_d0/1 +TTATGATTGTAGCTTTATCCCAAGAGGCAATCTTAAGATGATGAAATGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_74520986_74521432_1:0:0_4:0:0_d1/1 +GAAGAGTGGCCTTAACGTTACTCTGTTGCTGATAGTGACTTTGAAGTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_194568812_194569255_1:0:0_0:0:0_d2/1 +TTGAACTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_173094678_173095086_1:0:0_0:0:0_d3/1 +TTTGTGTTGAAGTGAAATGTAGATATAATTCAGGTTAAACCTAGGTGATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_125473775_125474200_1:0:0_0:0:0_d4/1 +TAAGAAAAAAACAACAAGAATAAAAAAGGGTGGGAGAGATCATGCCATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_60312834_60313394_2:0:0_1:0:0_d5/1 +TTTCTCTTTCATTCTCCTTTTACTACAAGTTATCCACAGAATCTCTTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_21769340_21769783_1:0:0_1:0:0_d6/1 +ATATCATGTCAGTTCTTTTGTGATTGGGTTACCTCACACAGGATGATGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_29011734_29012196_0:0:0_0:0:0_d7/1 +ACAAGTCTTTAGTATTTATTTTTCTAAGCTTGTTTTAATACGTTAGGTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_55988735_55989188_1:0:0_0:0:0_d8/1 +CAGAGGTTAGCCGTAGGTCTCGTTCCTGAGGAACTGTCCACCTTGGTCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_143689772_143690244_0:0:0_2:0:0_d9/1 +CATACTGTTTTTGGGCCTGTGCAAGAAAGAATCTGGCATAAAGGCATATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_102292799_102293241_0:0:0_2:0:0_da/1 +AAGGTGCTTGCTCATTTTCATAATATAATGCAAAGTCTTCAAGTCTCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_175815890_175816392_0:0:0_1:0:0_db/1 +TTTGGAAGGGTGAATTTAAGGTTACCTTGCTTCAGTCTCCAGATGTGACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_65030887_65031423_1:0:0_0:0:0_dc/1 +GTAAAACCAGCAAGGCCAACCCCAACTAAGCAAATTCATATTGGCTCCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_77446136_77446727_1:0:0_0:0:0_dd/1 +AGTCCTTTTTCCCGCTTGTCATTATGGGAGACGAAGAGGAGGCAAATTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_79825884_79826306_1:0:0_0:0:0_de/1 +AATTCATGGCTTCTCTCTTGAAAAACAAATATTATTCTGAAGCAAACTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_142137580_142138145_0:0:0_1:0:0_df/1 +GAACACACAGATTTTTTTTTTTTTACTTGAATCTTGAGAAATAGTGGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_77524851_77525306_1:0:0_2:0:0_e0/1 +CAGAAGGTGTACGTGTGTGTGTGTGTGTGTTTGTGTTGGGGGTGGGGGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_26694201_26694676_0:0:0_0:0:0_e1/1 +TCCTACCCAATTTCAAAGCTATATCAGCTTTTTAGATATTTTGAGAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_93157579_93158060_0:0:0_1:0:0_e2/1 +TCCTGCAGGCCCCTTACTTGGCTGAGGCACAGTCCCACCTTTTAGAGCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_93554302_93554745_0:0:0_1:0:0_e3/1 +TGAAGCAATTCTGATTTGAAATTAGTGCTGCTGGTGATAAAAATGCAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_115859373_115859816_1:0:0_1:0:0_e4/1 +TAGTTTTCAGTCAACTGTGAACATACTAAAGGTCAGAAGCCTTGATAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_59908209_59908731_3:0:0_0:0:0_e5/1 +GAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_154628329_154628794_2:0:0_1:0:0_e6/1 +ACGAGGATTAAAGGTTTAATACATAAGCCAAAGACACATTTGCTAAGTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_38934187_38934653_1:0:0_1:0:1_e7/1 +TGTTTACCCGAAAAGTATTTGATGCTGCCAGAGGTTTAATTAATGACAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_176440703_176441215_3:0:0_1:0:0_e8/1 +GCCTTCTCCCTACCACTTTGGAACCTTCTCAGAGAGGGCAGCCCTGATCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_146248574_146249007_1:0:0_0:0:0_e9/1 +TAATTTCAATTAAATTGACATTTATAAATATATTAGGTAATCCAAAGTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_137417062_137417534_1:0:0_0:0:0_ea/1 +CATAGCACCTACCCTTCTGTAAATGAAAGTTTGAAAATAACAGTGTAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_55607180_55607772_1:0:0_0:0:0_eb/1 +AAAGGATAAGATTTAACTTCACTTAAACTTTCATCCTCTAACATCACATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_174928179_174928755_0:0:0_1:0:0_ec/1 +TTTACTTTGAAGAGGTCATGGTGGGTGTATTAATCAGAATTCTCCTTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_113923154_113923648_3:0:0_1:0:0_ed/1 +AGAGCTGGCAGTAGACCTTAGTTGCCCTTGGTCTTAGCTGCATTGCCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_78423064_78423594_1:0:0_0:0:0_ee/1 +ACTCACAGTCTGTCATGGACACTCGGCCTGTTTGTTACTGTTATTAGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_154582561_154583019_0:0:0_1:0:0_ef/1 +TCAAGATAAATCAGGGATGAACATTAAATACTGCCGAAATTACAGGGCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_181723357_181723842_1:0:0_2:0:0_f0/1 +AAACTGAATTCTAGAGATTTCTCAAGAAATAAATCAGAGATTCTGTCCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_176206787_176207249_1:0:0_1:0:0_f1/1 +TTTCCGTGGGTCGAAGCATGCCCCTCTCAGAATCTTGATGACACCGCATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_156026308_156026788_0:1:0_2:0:0_f2/1 +AAATTTGGACCAGACAGTATATAAACAATTTTCACAGTGTTTGTATTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_55128175_55128671_1:0:0_0:0:0_f3/1 +GCCAACCAACTTCAGCTCCTTCCTCTTTCAGGAAAGATCACAACTTACCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_184447109_184447646_1:0:0_1:1:0_f4/1 +CAAGCCCTTCCTGCTATCCTTCAGGAAGAATGACACGGTTACAGCTCCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_194617734_194618226_0:0:0_0:0:0_f5/1 +GAACAGGATGGGTATATGTGGAGGAGTCACTTTCATTTAATGTACCCCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_80810218_80810755_0:0:0_0:0:0_f6/1 +TTCCCCACCCATCCCGGCTTTCCCACCCTAGCATTCTCCTACACTGGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_144296368_144296930_2:0:0_2:0:0_f7/1 +TGCATAGGAGAAACTGGGAAGGCGGGTAGCACTTGAAATGTAAATAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_108312503_108312946_1:0:0_2:0:0_f8/1 +TAAGATCAAGAATCAACAAATGGGACCTGATAAAATTGCAAAGCTTCTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_78228179_78228640_0:1:0_0:0:0_f9/1 +GGGAAAACAGTGAAAGTCACTTTGTGCTTTGGGGAGGCCAGGAGAAGCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_52088998_52089426_1:0:0_1:0:0_fa/1 +TGATTTTCTTTGAACTGATTAGAGGCATTGTAAGTTTTTTTTAGGATAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_30782403_30782942_1:0:0_0:0:0_fb/1 +GTGAGTGTGTGCCTGCTTTACATTGCCTCCAACTCCACATCACTTCCTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_6435675_6436268_3:0:0_2:0:0_fc/1 +CTGTTCTCTCCGAGGCGCAGCTTGCTCAGACTCTCCAAAAATACGCTCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_164237997_164238538_0:0:0_0:0:0_fd/1 +CAGGAGCCTTAACCTTCTCTTCTCTCTGAGAGGACTTTATATAAAACAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_187097969_187098475_2:0:0_2:0:0_fe/1 +AGAAAACAGGGGGTTGGGAGCAACCCTGTCCACTGTGTCGAGCATTGGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44694856_44695375_3:0:0_1:1:0_ff/1 +GTCGATAACTGTCAGGTCCATTTGTTTCATAACTTCTGTTAGTTTCACTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_111782668_111783223_1:0:0_3:0:0_100/1 +ATTGCTCTGTAGTTTATAACTGTGAAGAGGGCTATGTGGATAACTAATTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_94206847_94207360_1:0:0_1:0:0_101/1 +TATAACAGAGATACCACGAAGCCCTAATGTTAAAACTTACTTTTAGGAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_132119789_132120286_3:0:0_1:0:0_102/1 +GCATAGACCTCTGTCTTCAAGAGCAGGGCATAGGGCAACTAACACCATCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_34226734_34227203_0:0:0_0:0:0_103/1 +GAATTCAAAGCTAGCCTGGTCTAGAGAGTGAGTTTCGGGACAGCCAAAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_138105716_138106319_4:0:0_1:0:0_104/1 +CTACTATCTCAAGAGAGCTGTTCATGTGATAGAAATCAGCTAGTGCAATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_126030856_126031342_1:0:0_2:0:0_105/1 +ATACTCAGAACCCAGTTTTTAAATGTCAGGCATGGTGGCATTTGCTTAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_118807485_118808058_0:0:0_1:0:0_106/1 +AGCCACATTTATCCGTGTGTCTGTTCTCAGACAAGCCAGTGGGGGCCAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_19849114_19849606_2:0:0_0:0:0_107/1 +AACTTTCCATTGTAACAAAATACTGGACCAAAGACACTTGAGGAAGGCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_66877733_66878136_2:0:0_1:0:0_108/1 +TGAAGAGATGGCTCAGGGTTAAGAGCCCTGAGTGCTCCTCCAAAGGTCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_132522495_132522987_0:0:0_1:0:0_109/1 +ACTTCCCAGTTGACTTTGATAAGCCTGGAGGTCACTACCGGAGAGCCAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117050436_117050942_0:0:0_1:0:0_10a/1 +ACGGGTGGGGGGGCGGGCACTGGTTAGTGCCCTATAAGAGGAACTAACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_125967212_125967705_0:0:0_0:0:0_10b/1 +CTGTGCTCAGCATCCTCCTAACTCCTTCTGACAGAGGCACCGGGTCACTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_69313718_69314189_1:0:0_2:0:0_10c/1 +CACTGTTTCCTGTATCTAATCCATATTAGTGAGGACTATGATATTCAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_60897368_60897871_1:0:0_1:0:0_10d/1 +CTCAGCTATTAAAAACAATGAATTTATGAAATTCTTGGAACAATGGATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_174325015_174325549_0:1:0_2:0:0_10e/1 +CACATCATTACTTTAAATTTATGCAAATATCATTTTTAAAACTTAATCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_85055965_85056468_2:0:0_0:0:0_10f/1 +CCATCTATGGTCATTGAGAGTTTGGCTGGTTATAGTAGCCTGGGCTGGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_131415777_131416249_5:0:0_1:0:0_110/1 +AAGTTCGCGAGGGCTGACCAGAGGGCCACAGCGGGACAGGAAGGACCCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_67136277_67136702_3:0:0_0:0:0_111/1 +CTTTCACCATCATAAGATATTTTTGGAGCCTCCATCCTGTCAAACAGATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_8402131_8402528_1:0:0_2:0:0_112/1 +AATTGTCCCCTGCATCCTATCCGATCACCATGGACTAAGGCTGATCTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_155126875_155127345_1:0:0_3:0:0_113/1 +CGACAGCAAGTGAACGCATTGGCGTTTGGCATTCCTCTCTATGCATCCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_93916438_93916928_0:0:0_0:0:0_114/1 +GCAACCTTGTCCAGAGGGTGCTCAGAGCTGGCTCCTGGCTAACAGTGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_135734641_135735118_0:0:0_0:0:0_115/1 +CCCCTGCACTGGCAGGTCCTTGGGTTTCACCCATTCCCCGCTTCCCCCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_44391025_44391499_0:0:0_1:0:0_116/1 +GGGAACCCTGAACCCCTCAGGGTGGCGGGAGGCGTACATGGAGCCAGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_110722550_110723095_2:0:0_4:0:0_117/1 +AATCTATAAACCCAATAATAGAAAAATGAAAAAATTCTTCAACACATGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_185586471_185586808_1:0:0_0:0:0_118/1 +TGGCCATCAAAATTCCAGAAGGCTGCTTTGTAAAAACCGTTCATTCTCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_182936908_182937483_1:0:0_2:0:0_119/1 +ATTGAGCTGTACTTAAGCACAATTAAAATGTAAAGATGTTGATTCCTGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_136882207_136882635_0:0:0_2:0:0_11a/1 +CAGGAGCAAAGCTCTCCCTAGCTGGACTGGTAATCTGTTGTCAACTTGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_22027558_22028086_0:0:0_2:0:0_11b/1 +TAATGTTTGCACATAAGTCTCTGCATGTTTTCCCATTGGTTCTTGTTTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_101069088_101069523_0:0:0_0:0:0_11c/1 +GCTCTGGGGATACCGGTTAGTTCATATTGTTGTTCCTCCTATAGGGTTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_133430180_133430643_0:0:0_3:0:0_11d/1 +TTGGAGCTTGAGTAGTCGATAGTTGTGAACCACCATGTGGATGCTGTGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_141505317_141505766_0:0:0_2:0:0_11e/1 +AATGGAATCTTCTGTACCTGAGATTCTCTCTTTCAACTCTTGTATTCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_103387516_103388014_1:0:0_1:0:0_11f/1 +TGAAGTCTCTAAAGACCAAATCATTCCCTACCCGTCTCTCTCTTTTGTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_134753416_134753860_0:0:0_1:0:0_120/1 +GTGCAGCCAGGGCACCTAGCCCATGGCCTCCAGCCGGACTGAGACAGCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_168048225_168048764_3:0:0_0:0:0_121/1 +AGTCGGCATCCTCCCCTTCTTTCTAAAGACTCCCTGTACCAACATTTCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_15110325_15110842_0:0:0_1:0:0_122/1 +GGAACCTATAGTTTCCAATGGTCATCAAACTGTAATTAAGTAATTTATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_71511848_71512298_1:0:0_1:0:0_123/1 +AAACACTGGGAGTGCCTGCATAAATCTTTTACCATAAATGGTAGGGAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_37275066_37275622_2:0:0_0:0:0_124/1 +ACCCCGAGTTCCCCAACATTAAAAACATGATCATGCCCGGAAGAAACAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_191970326_191970894_1:0:0_0:0:0_125/1 +TATAGAACCTGGTCTATGTACCCTGAATCTGGATACGGCCTTCTGCCTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_137258018_137258449_1:0:0_1:0:0_126/1 +AACCTATGTTAGGCTGGAACCCCTGCTTGCCCTACACAAGCTGGGAAACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_163885263_163885763_1:0:0_0:0:0_127/1 +CTTCATGTATTTAAAAGTTACTTATTTTTCTACCAGTGATCACTGTTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_95122061_95122611_1:0:0_2:0:0_128/1 +TTTGGGTCAAGTTCTCAGGCTTCATTTTTTTTAGGTGGCGACCAGTCCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_191245641_191246131_1:0:0_1:0:0_129/1 +GTTCAATCCTACCTCTGTTAACAGGCAGCCAGATAATTAATCTGTCATCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_11721955_11722368_1:0:0_3:0:0_12a/1 +ACATTTGTTAAATCAACTGAGAGATGTAGACACTCTATTAAGTCACCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_102954712_102955237_1:0:0_1:0:0_12b/1 +TTTTTCTTTGATTGGTGGTTTAGTTTCTGGTAGCTCTGGGGATACTGCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26914346_26914925_0:0:0_1:0:0_12c/1 +TTTAGATGATCCCAAAATGAGATTTAGAATGTCTTCCTTTTGCACTTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_151053369_151053909_1:0:0_0:0:0_12d/1 +GACTTTAAAAAAGCCTCTGAGGAAGCAACATTGAAATTGAAAGTTGCAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_93621447_93621970_1:1:0_1:0:0_12e/1 +GCCCCTGGAATGGGCCTCATAAAAACTCTAGGAGGGCTTCTGCTGCCCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_13530953_13531445_0:0:0_0:0:0_12f/1 +AGAAAAAGGTCCATTTCAAAGAAATATTTGTTAGTAATTTAGGACAGAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_154530120_154530631_2:0:0_4:0:0_130/1 +ATGCTTTCTAGTCTCTAAATGGCCTCCTGAAACCAGAGAGTGAACTTCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_100109085_100109588_0:0:0_2:0:0_131/1 +TTGTCATTATTTGTCTGGATGCATGTTGGCATGAAAGTTAATGATGTGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_150348101_150348543_0:0:0_0:0:0_132/1 +AAGGAACTGAAATCCTGCCCTGTAGAAAAAATTGAGCCTTTAATGGCTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_8725925_8726392_0:0:0_3:1:0_133/1 +ATTCAGGTGACAACATATTCAGTTGAGGATATGGAGAAAGATGACCACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_189147844_189148204_2:0:0_1:0:0_134/1 +ATTGAGAAATATGCAGGAAAGATGGAGTAACAAAGATCCTTAAAAAAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_45618673_45619149_2:0:0_2:0:0_135/1 +ACACTGCATGATATGGAGTCTATCCCAGGCATCAGTGAAGAGGCCAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_104062147_104062721_1:0:0_0:0:0_136/1 +ACATACATATATATACATATATATATATATATATATATATATATAGAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_138405158_138405766_1:1:0_1:0:0_137/1 +TCAACACAATGACCCTTCTTGCTTTAGAGTCCTGCAGTTCATGTATTTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_115548969_115549503_0:0:0_1:0:0_138/1 +AATTGATGCATCCCCTCTTGGTCCCCTCTCACACAGTCACTACCCCATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_195151172_195151687_0:0:0_0:0:1_139/1 +ATTTGGGGCTACTGTTGACTCTGGAATGTGAGGATGGGTATACCTTGGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_138103424_138103925_0:0:0_0:0:0_13a/1 +CTACTAGAGAAACTACTTCCTCACGTATTATTGAGACTTCCATTGTGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_84481564_84482032_1:0:0_0:0:0_13b/1 +GTTACAGAGACAAAATTTGGAGCTGTGACGAAAGGATGGACCATCTAGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_180211651_180212100_2:0:0_1:0:0_13c/1 +AAAGCCATCTGTTTGACATGAAAACGGGGGAGACACATGATTTGGGAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_19484875_19485375_1:0:0_0:0:0_13d/1 +CAACCACTCTGGAAATCAATCTTGTGGTTCCTCGAAAATTGGACATAGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_8815773_8816268_0:0:0_1:0:0_13e/1 +AAGTTGTTTCCATTAAAAAGTACTGATTTTGAAAACTAATAAGTTAAAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_118367902_118368405_1:0:0_0:0:0_13f/1 +AGTATCTCAGAGAACTCACTGTATAACCCAAGCTAGACTCAGAACCTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_83281820_83282310_2:0:0_3:0:0_140/1 +TTTTACCAGTTCTTCATTTGAGTCAGGGTCTCTCTCAAACCTGGACCTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_24810903_24811377_2:0:0_0:0:0_141/1 +ATAAACAAGGCTGCTATGAACATAGTGGAGCATGTGTTCTTCTTACCGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_24847990_24848482_1:0:0_1:0:0_142/1 +GTGCTTACAAAGGCAGGAAGATTCCTGAGTTCAAGGTCAGCGTGGGACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_25453923_25454484_1:0:0_2:0:0_143/1 +CATCTGTGCTTTATAGTGCTTCTCATTCGCTGACAGGGATAGCCTCCAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_35396075_35396608_0:0:0_1:0:0_144/1 +TTAGTGGAACATCCCTGGCTCCACTCTGTGTGTGTGTGTGTGTGTGTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_184356181_184356676_1:0:0_1:0:0_145/1 +GGGAGAGTAAGTAACTGCCTTCTTGTATCAGCCCCAGTTTGATGCTTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_87890172_87890679_0:0:0_1:0:0_146/1 +GGAGCAGAGCTGATGGAGCATGGATCACTGTATGATCAGAGAATTAATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_192825121_192825655_0:0:0_3:2:0_147/1 +CCACATGGTGGCTCACAACCATGAGTTTCAAGGAATCTTCTGGCCTTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_29477154_29477657_0:0:0_0:0:0_148/1 +CTTCTCAGCCATTTGATATTCTTCAGGTGAGAATTCTTTCTTTAGCTCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_68360607_68361138_2:1:0_2:0:0_149/1 +ATTGTTAGGCAGAGATCCAATATATGAAATTGTGCTTTTCCTGTTGATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_90679374_90679891_2:0:0_4:0:0_14a/1 +GCCAAGGCACTTGTGTGTTGGTTAGAAGATAACTTTTGGAAGACAGTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_90921852_90922384_0:0:0_1:0:0_14b/1 +CTGGATGAGGCGCCGAGATGGGGAAAAGGTTGGACCTTTCCACGCTCACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_144744406_144744790_0:0:0_3:0:0_14c/1 +TATATCTTGGGTCTCCTATGTTTGGGGCTAATATCCACTTCTCAGTGAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_157579434_157579959_0:0:0_1:0:0_14d/1 +CATAATGTTGTTCCATCTATAGGGTTGCAGGTCCCTTTAGCTCCTTGGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_22354013_22354577_0:0:0_2:0:0_14e/1 +TTCTGTAGCTGATAATACATCATTGTGTTGGCATATCTCATTTTAATACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_14011029_14011557_0:0:0_1:0:0_14f/1 +AAAAATGTCACATGCAGAAAACAAAGACGCCTTCCTTGGCAAACACTGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130418472_130418955_2:0:0_2:0:0_150/1 +TGACATGGATGTCCGAAATTCCGATGGTGAAACACATCACTATTATTATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_150912771_150913298_1:0:0_0:0:0_151/1 +CTGTTTAGAAAAGTTTTATGATGTTTAGAAATCATGCATGCATAATACTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_122600000_122600452_0:0:0_0:0:0_152/1 +CCCCATTTCAGGGAACAGTAAAGGCAGGAGGATCCCTGGGGCTTGCTGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_172852130_172852552_1:0:0_2:0:0_153/1 +AAAAATGTACAACATCCTTAATCATCAGGGAAATGCAAATCAAAACAACG ++ +22222222222222222222222222222222222222222222222222 +@chr1_58219252_58219809_1:0:0_1:0:0_154/1 +CAGAGGAAGCAGAAGAGATACACTTCCATGTCGGGTTCCTAAGTGATCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_154116562_154116985_0:0:0_0:0:0_155/1 +TGACCATGCCAACCCAGCTCGAGAGCTTTTTTCCTCTCTTTAACATCCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_169424620_169425179_1:0:0_0:0:0_156/1 +ATAGTATGGTGGATGAGTTAAGAGTAAGTTTCAAAGCTGGGACAAATGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_72776580_72777093_1:0:0_0:0:0_157/1 +GATATCCCTGAGTTGTTACTCTGTTTCATCTGGGCTGTTCTTAACTCCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_102420738_102421205_2:0:0_1:0:0_158/1 +CATTGCCAACTCTGACACATGTCAAGGAATTCAGAGTAGAGAGCATATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_148315363_148315906_2:0:0_0:0:0_159/1 +CATGGAAGGAGTTCCAGAGACAAATTTTGGAGCTGTGACGAAAGGATGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_93257911_93258453_0:0:0_1:0:0_15a/1 +ACACCGGGCAGTTCTCATTGCATTGCAGCGAAGGACTTCTGCCATGTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_94169994_94170446_0:0:0_1:0:0_15b/1 +CCTTGACCTCCTTTTCCTCAGGTTCTTCTCGTTTTAAATGAAAAATTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_126263407_126263894_2:0:0_2:0:0_15c/1 +GATTAGACTCTCGCTGCATTATGAAAAAAAAATTATGTGCATGAAGGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_42763327_42763896_1:0:0_0:0:0_15d/1 +GTCTAAACATTCTAGTCATCAGAATAAAGTCAGAAACAGAGGCTGGGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_127932894_127933379_0:0:0_2:0:0_15e/1 +GTCAGCAGTGCAGGATTATCTATCTATCATCTATCTATCTATCTATCATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_83608654_83609158_1:0:0_3:0:0_15f/1 +AGACACAGTAAGGAGCAGAGACTGAAAGAAAGGCCATCCATAGACTCCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_47669914_47670464_0:0:0_0:0:0_160/1 +CCCAGGAGTTGTATAGCTGGTGCTTGAGGCACACTTGCTGAGAAGAGGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_133731323_133731869_1:0:0_2:0:0_161/1 +GATGCTTGTGAGACACTGGGCAATGCCACAGCCATTTGCTCGGATAAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_133255321_133255920_0:0:0_1:0:0_162/1 +TCTGGAAAGGTTCAGGCTCAAGGAACTGGAGACAGATTTAACCCCACATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_23328420_23328852_0:0:0_1:0:0_163/1 +AGGAAGAGAAAAGATATGCTAAGAAACCAGATGACAGGCTCCAAGAACGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_53072730_53073291_2:0:0_0:0:0_164/1 +TACGACGTCCACTTATGAGTGAATATTTTCAGTATTAATGTAAGGTGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_173130259_173130757_3:0:0_2:0:0_165/1 +AATTATTTGGAGAGCACTCAGCAACTAAGAAAGTGATTTCGTACACAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_87397192_87397710_2:0:0_1:0:0_166/1 +GATGGGGTTTCCTTTCACTATTTAATAGAGAAATATAACGTTACTTTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_187438711_187439219_1:0:0_1:0:0_167/1 +CATTTGGTCTGGACAGGACGGCAATAAATAAATAAATAAATAAATAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_123461089_123461580_0:0:0_1:0:0_168/1 +ATACAGCTTTCTGCATGTGAGTATTGTATGTGCACATTGACGCCTAGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_181088135_181088642_2:0:0_2:0:0_169/1 +ACACTTTTTTTAAAAAATAAACATATTTTTATAAAACAAATGGACTATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_167764494_167764902_0:0:0_1:0:0_16a/1 +CTTTTGCTATTGTTCTATAGTATGCTTCTCCAGTGTGAACTTTGTATATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_157283727_157284210_1:0:0_0:0:0_16b/1 +GCACCCCAGGAGCTTGACATACCGTTCCCTAATTCCTACCTCTTCCCTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_156428357_156428913_4:0:0_3:0:0_16c/1 +TCTCCCTTCCAATGTAGGACTGATCATGGCCACCCTTCCCCCTCACCCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_27945156_27945679_0:0:0_2:0:0_16d/1 +GCCTTGTCTATCTACTGGAGGTCATCTCTTCAATTTCCATCTCCCCCCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_190959090_190959565_0:0:0_0:0:0_16e/1 +TATTCCCTAAATAATATGGAGTTGAACAACTATCAAGCTTCAGGCATTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_163184140_163184589_0:0:0_1:0:0_16f/1 +ATTAGACACCCCAGTCAGAAAAATGATGCACGTTAACGAAGATAAATGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_104189461_104189906_1:0:0_1:0:0_170/1 +ATTGAAAAACAGAACCTCATAAGATGGAAAGCTTCTATAAGGTAAAAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_77562742_77563170_2:0:0_0:0:0_171/1 +TATGGTCCAAAATAAAGCTCTCTTTCCTTATGTTTCTTGGTCCGAGTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_192763088_192763581_0:0:0_0:0:0_172/1 +TGTCAGAGTATTCTATCACATCAATAGGAAACGAAACCAACGCCCACTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_36839841_36840369_1:0:0_1:0:0_173/1 +CAGAGGGTAAGTTTAATGTTCATTTTGGTGGGAATTAGTGCCTAGCAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_114603035_114603542_0:0:0_0:0:0_174/1 +CACTGGTGAGCCTTCCAATTCCGGATTGTAATTCATTCCAAATATTGTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_57790506_57791066_2:0:0_0:0:0_175/1 +GTGGAAACTTGAAGTATATTGGGGTATACCCGCGCCAAAGGACTATTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_35650713_35651282_0:0:0_0:0:0_176/1 +TAAGAGCCAGCTCCCACCTCCAACTCACAAAAAAAAAAAAAATCAACAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_9711969_9712380_0:0:0_3:0:0_177/1 +TTATTTTCTAGCTTTAAAAAACAAAGATTTATTAATATATTTATTTAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_89016556_89017046_1:0:0_0:0:0_178/1 +AATAGTTAATATACATATTATGTTCTCAGAAAATGCTAAGAGTTTATATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_132197564_132198148_2:0:0_2:0:0_179/1 +CCAACATGAGTTCGGAGCAGCAATCACATAGGAATTAAAAGCCATAGGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_104335733_104336245_1:0:0_3:0:0_17a/1 +AAATCCTTAATAGTAATATTACTGTATTAATTTTTTTACCTTATATACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_75633066_75633602_2:0:0_1:0:0_17b/1 +ATTCTTATGTTTATTGGTTGACATTGGCTGTCAACTTGACAGGATCTGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_189869166_189869657_0:0:0_1:0:0_17c/1 +TCGGCTCTGTGCCACGGTTGGAGACCCCTGTTTGTGGTGTGGTATCGTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_27940779_27941192_2:0:0_0:0:0_17d/1 +CAATAAAATACTCACAAACAGAACCCACAAACACTTCAAAACAATCATTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_116796056_116796571_1:0:0_1:0:0_17e/1 +GGCTATTCTGAGGCCTCTGGTAACTATATAGCAGAAGACTTCCTGGTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_20487571_20488054_3:0:0_1:0:0_17f/1 +AATGGCGTGGAACTTGAGCCTGCGGTACATAGGTAAGCAGGCTACCCGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_70106451_70106893_0:0:0_2:0:0_180/1 +TATGTCAATAGTTATAAACAATGTCAGTGTAAAGCAAGTCTTGTGCAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_138350547_138351128_3:0:0_0:0:0_181/1 +ACCTTTTTTTTTCCCTCTGTGTATTTTTTTTTATTCCTCCTGTATCTCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_103571822_103572343_2:0:0_1:0:0_182/1 +GCCACCCAAGTGCTCGACTTATACTATACGTAGGACAACCTTATACATAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_185391115_185391738_5:0:0_0:0:0_183/1 +TTGAAGATCTTTGAAATGTGAGTAAAAATGAGAAATTTAACAGAAAGTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_121389447_121389902_0:0:0_0:0:0_184/1 +GCCCATTTCCTGTTGGCTGCACTTGACTTGGGGTGTTTAGGATCCATTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44088278_44088819_1:0:0_1:0:0_185/1 +AATACTTAAAAGAGTGAAGAAATTGTTTTTCAATGAATCAACTTTAAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_57600248_57600747_0:0:0_3:0:0_186/1 +GTTCGGAACTCATAAGCACATTGAGACAAGGCCATAGCCAGTTCAGACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_105765709_105766274_0:0:0_4:0:0_187/1 +ATGGTGACGTAATACTGACAGCTGCTTAGAGCTGTGGCCCTGACCTGTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_158039847_158040318_0:0:0_1:0:0_188/1 +CCCCTTGTCTGAATACATCTGCCATCCCAACCAGCCTCAAGGAAGCACCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_100649250_100649781_0:0:0_0:0:0_189/1 +TTAAACACTGTCTATTCATGTATTCATTTGTGTACTTCAATGTAAATGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_92627120_92627576_1:0:0_1:0:0_18a/1 +ACAGTGGAAACCAGCCATCACTGATATGCTGGACCAAGATGGAGAAAGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_47045474_47045999_2:0:0_2:0:0_18b/1 +GCTAGGTCCAGGTGCTATCCTCTTCACTGACAGGTGTAAGAATCTATTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_58859721_58860237_3:0:0_1:0:0_18c/1 +GTGCAGAGTGTCAGCTGTGTGGGAACCTCACTTCCCTCTTCCCTTAACCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_38899259_38899748_1:0:0_2:0:0_18d/1 +GACAGTTAATGGGGAGTAGACCCCATTATCTCCAAGGCTGTTCTCCTGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_43169971_43170448_3:0:0_0:0:0_18e/1 +CAGGTGAGATAAAGAAGAGAAAGTAGAAGGGCTTATCTGAGCCACAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_169159076_169159522_0:0:0_2:0:0_18f/1 +TTTACATTGCTGACAAATTCATTCGGATACCTGTGTGAAATTTGGATTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_14622737_14623201_1:0:0_0:0:0_190/1 +TCTTCATCTTGGAACCTGAATCGTGTTCCATTCCAAACCAAAGGAGGTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26821729_26822157_1:0:0_3:0:0_191/1 +AGTTATCAATCATTTTACTTTCTTTTAAGATGTACACCTGAGGTGGTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_146737011_146737509_0:0:0_0:0:0_192/1 +AATATTTTCTAAGATTCAAAATTGTGTATTTTATTATTGTTTTAAAAGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_132937628_132938130_1:0:0_0:0:0_193/1 +TCAGGGAGATTTACCAGAGCAAACTTGTCGATGGAGACCAGTTCCTCCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_108674541_108675003_0:0:0_0:0:0_194/1 +TGGTTGTCCAGTGTCAAATAGTCATTCCTGAGCATATATATGCTAGACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_155314929_155315340_1:0:0_2:0:0_195/1 +AGGAAAGGAATTTTAATTATAACAGTATCTAAAAGAATTAAACATTTAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_76995369_76995845_0:0:0_0:0:0_196/1 +GGGTTGCAGATCTCTTTAGCTCCTTGGATACTTTCTCTAGCTCCTCCATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_88758655_88759125_1:0:0_1:0:0_197/1 +GAAACCTCTGTCTGCTGCTTTGTCCAGTTTGACCTCCTTCTAGCATCTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_179447008_179447452_1:0:0_1:0:0_198/1 +TGGTTTTAATAAACCTGGCCCGCATAGGCCCATAGGGAGTAGCACTATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_70539778_70540384_1:0:0_0:0:0_199/1 +GAAAAAAGTGGCCATGAATTTGGAAGAGATCAAGGGAGGGGTATATGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_171297998_171298490_3:0:0_2:0:0_19a/1 +GTATTCTAACGCGACTATGCTGGCTACTTCCCGGCCATCTGCCCCTTCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_4703882_4704398_1:0:0_1:0:0_19b/1 +CAATTGAACTCTGCATCTGGTGAGGTATTTTACACCCATTTTTGTAGCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_148373552_148374029_0:0:0_2:0:0_19c/1 +TTCCAGCATTTTCAATATACACTGCACATGTCTTTGCTGTGGTACAGCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_165037832_165038374_1:0:0_2:0:0_19d/1 +TAGTGTGGACACCAACTGCTACAGATGTGCCAAGCCTTCATCTCAGGTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_117911191_117911633_0:0:0_2:0:0_19e/1 +GTGAACTCCAGAAAAATCAAATAAGCCTATTAAAAAATGGGGCTCAGAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_101942751_101943298_2:0:0_2:0:0_19f/1 +CACCTAATGTTTCCTGTTAGATTACACTACTGATTTATGTTTTCACAGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_159291114_159291545_1:0:0_0:0:0_1a0/1 +TATTTGCCTTTATAAGAGCTGCCATGCTCATGGTGTCTCTTCATAGCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26628880_26629394_1:0:0_1:0:0_1a1/1 +AGCCATGTGAATGATTGAATGCGTGAATGAATAAATAAATAAATAAATAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_18997387_18997869_1:0:0_1:0:0_1a2/1 +ACTTATTAGTTTTCACTGAAGCTAACCATGCCATTGCTTCCTATTTTGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_39575593_39576071_1:0:0_2:0:0_1a3/1 +TCTTCCTGTACTGCATTTTTGTTCTCGTTCAGTTATGGTGTGCATGCGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_5509844_5510306_2:0:0_1:0:0_1a4/1 +GGATCTTCCAGCCCAAAGTTGCAAAGTCCTTCCACAGTCCTCCCCAAAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_109704460_109704956_1:0:0_0:0:0_1a5/1 +TAATTACACAGGAACCAGCAAACCTGCCTGTAAAATGGTGAAGGTTTCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_156587931_156588493_1:0:0_1:0:0_1a6/1 +AGTCCTCCTACAATTTGATATGCCAAGGCTGTTTGATATCCATGGGAGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_176610586_176611106_1:0:0_0:0:0_1a7/1 +AGTGAGGCTTCTTGGTTCCTCCTTTTTCCTGCTCATTGGAACATATTTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_180872448_180872981_1:0:0_3:0:0_1a8/1 +AACAGCAGCTGGGCATGTTGGCCCACGCCTTTAATCCCATCACACAGGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_26474215_26474717_2:0:0_1:0:0_1a9/1 +TGGCACGAAGCAGCACAAGCGCAGGCCCGAGCAAACGCAGCTGCTTTGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_104541278_104541749_1:0:0_0:0:0_1aa/1 +AAAAAAATTAAAAAGAGAAAGAAAACAGATGGGGACACTTTCTAGAATGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_67015960_67016373_2:0:0_1:0:0_1ab/1 +TAGTTTTGCCGAGACAGAGTAGGCTCGTCTTTAATATTCGTTTATCTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_29940243_29940732_0:0:0_1:0:0_1ac/1 +ACTGCACTGAAGCTGTTTATCAGGTTTAGGAGTTCTCTGGTAGAATTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_193079402_193079850_1:0:0_6:0:0_1ad/1 +AGGACCCAGACTTGATTCCCAGCATCCACAGGCAGTTCCCAACCACCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117439972_117440528_1:0:0_0:0:0_1ae/1 +CAGTACCAGGAGATTTCACCCCTGCTTCTTAATTCTGAATACATCTATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_177239334_177239795_2:0:0_1:0:0_1af/1 +TTTTGAAACACATGGCTAGCAGATACTAGTATAGCAGTAGTAGACTAATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_158414545_158415096_3:0:0_0:0:0_1b0/1 +ATTGTAACAAGTACTTTTTTTTTCTGCTGAAATAAAGCCATTACTGGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_97093485_97093964_1:0:0_0:0:0_1b1/1 +GTACACTGGCTGATTTAATCCCACAGTTTTTTTCTTTATAACCTAATGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_67614138_67614777_0:0:0_0:0:0_1b2/1 +GGCCTTATAGAAACACTAAGTCCTAAATATATTTCTCAAGGGAATTTTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_153549562_153550076_0:0:0_1:0:0_1b3/1 +ACGCGGGTCTGCAAAGAATCCCCGAGTGTCACTGGCCCCAGGCGGCAGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_55425424_55425904_0:1:0_0:0:0_1b4/1 +CAGTTATAAGTGATGGGCTAAGAGGATGCTATGTGTTCTATGAAAGGCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_191019412_191019908_2:0:0_1:0:0_1b5/1 +ATATGTGTGAGTTGGGTTCTGTGTCAATGAGTGCAGTGCCTATGGAGATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_73180421_73180945_2:0:0_2:0:0_1b6/1 +AGCAGCCTACTTCCAGCTCAATATGACTTCATTTTAACTAGTTTATCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_38129466_38129932_2:0:0_2:0:0_1b7/1 +CGCGCCGCCCCAGGCCACCATTCCCGGGCCCAGCCTCTTCCTCGGGCCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_133540103_133540570_0:0:0_0:0:0_1b8/1 +ACAGAGAAACCCTGTCTTGAAAAAACAGAACAAACAAAAAACCAAGCAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_184916633_184917139_2:0:0_2:0:0_1b9/1 +GCTAGGACTCTTAACGACCTTGCCAGCCCTCTGTACGAGTTACAGTTAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_175669652_175670114_1:0:0_1:0:0_1ba/1 +AGACAGACAGCAATTTAAATAGGCCTCTGTCCAGCAATGGGGAATCTAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_8296849_8297319_1:0:0_0:0:0_1bb/1 +ATAACAGTAGCAAGAAATAAAGTATAATGTGAAATAAGTTAACTTCTATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_152905590_152906078_1:0:0_1:0:0_1bc/1 +TTTGTTTGGTTGTTTTAGTTTTCAGTCTGTTTTGTTTGTTTGTTTGTTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_114902352_114902833_0:0:0_0:0:0_1bd/1 +CACCCCAGTCCCCTACCCACCCACTCCCACTTTTTGTCCCTGGCATTCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_192964279_192964734_0:0:0_0:0:0_1be/1 +GTAAGTGTGTGTGTATGTGCAGACAGAGACTAGAGAACAATCATGGATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_38321189_38321768_1:0:0_3:0:0_1bf/1 +GCCTCAGTGTAACAGTTGGCAGCTGTTCCGTGGGAACAGTAACCCATTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_78900626_78901065_0:0:0_0:0:0_1c0/1 +ACTTTAAAACACAGTGAGTGGGCAATAACACTTAGTAAGACCAGCTATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_113540760_113541176_0:0:0_3:0:0_1c1/1 +TTCCCACCTCAATACACATACACACACACACACACACACACACACACACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_130677359_130677835_0:0:0_1:0:0_1c2/1 +GAGCTGAAGGGGTCTGCAACCCTATAGGTGGAACAACAATATGAACTAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_180204210_180204758_2:0:0_0:0:0_1c3/1 +TGTGGCTCAAACTCCTCTCCAAGCTGACTGATTCCATCTGGCTTCTCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_192984278_192984850_2:0:0_5:0:0_1c4/1 +GAAGTGTTGTGGCAGTTTATTTGCTTTGCGTTGTGATCTAAATCAGACCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_176155520_176156071_0:0:0_4:0:0_1c5/1 +GAAAGAGGAAGCTGAAAGCTTGTAAGAGCCAAAGAAACAGAGTTTGCTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_11299746_11300227_3:0:0_1:0:0_1c6/1 +CATTCTTTCCTTCTGAAGGATTTATGATAATATTGCCTGTGCATATTATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_40475921_40476533_1:0:0_0:0:0_1c7/1 +GTCATAGTTGTTTACTAGACACAGAAACGTCTGAGTGTCAGAAATATGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_161162459_161162939_0:0:0_0:1:0_1c8/1 +ACAGAAACTCGTCCCACACAGTAACCCTTAGGTGCATTTAGCTCTCAAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_56968239_56968712_1:0:0_4:0:0_1c9/1 +ATGGATTTCCCTCCATTGTGTGCATAGAGGTGTCCAAAAAGTGAGGCTCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_90357627_90358090_2:0:0_1:0:0_1ca/1 +TAGCAACTTATATTCTCTCAGGCAATGGTTTCTTTTTTCTGTTTGAAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_184900782_184901265_1:0:0_1:0:0_1cb/1 +CGTTAGTTGAACAACACAAGCTTGTGTTTAGCTGCAAGATTAACATGTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_34520052_34520514_0:0:0_0:0:0_1cc/1 +TGTCCTGCTCCTGCTCCTGCTCCTCCTCCTGCTCCTCCTCCTGCTCCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_121381246_121381739_0:0:0_0:0:0_1cd/1 +CTGTGTTCAGTACAATGCTATTTGTAATCCTTTAAATCCACCCCTTTGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_80355344_80355825_1:0:0_3:0:0_1ce/1 +ATATATCCTATCATATCATCTGCAAAAAAATGATATTTTAACTTCTTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_23025664_23026100_0:0:0_2:0:0_1cf/1 +GGCCCTCAGGATTCAACAGGTAGCGTGGCTGCTCAAACACTTTCTTAGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_126877190_126877687_2:0:0_0:0:0_1d0/1 +GGACAGAGTGGGTTATGTTACAAGAAGCACTCAGACATTGAAATCGGAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_64317525_64318044_1:0:0_0:0:0_1d1/1 +TGTTTTTTTTCTTTTCTGTTGAGGGGTTGTTTCTTACCACAGGGAGTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_41387597_41388152_2:0:0_4:0:0_1d2/1 +AGCACTATGTCTGCGTAGATGCTGCCAAGCTCCTGGCTAGATGATAATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_179273458_179273967_4:0:0_2:0:0_1d3/1 +GTCCTCCCTTCTTCGTAATTGTATCCTGTGGTTACATTTTTTTGCCTGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_159718146_159718573_1:0:0_1:0:0_1d4/1 +AAAATGTCAACAATTGTTATCCGAAAGATTATTAATCTTTTTGCTACTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_77989741_77990190_3:0:0_2:0:0_1d5/1 +GCTCCTCCAATGGGGTCCGTGTTACTCATCCAATAGTGGATGACTGTGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_70921539_70922106_2:0:0_0:1:0_1d6/1 +ATATGCAAAATTTAAAACTGTTGATCTCATGGAACAAGTTGAATAATTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_135807545_135808030_2:1:0_0:0:0_1d7/1 +CAGAGCACAGTGTGCATACTGGGACCCCCATTTTGTGACCCAAGCCCAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_140999216_140999698_1:0:0_1:0:0_1d8/1 +AATGCTTCAATTAAATAACCAAAACCTAGGTTAGTCATTGAGGGTATCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_148512883_148513388_0:0:0_1:0:0_1d9/1 +CTAAGAATACCCAAAATATAAGATACAATTTGTGAAATACATGAAACTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_95472009_95472435_1:0:0_0:0:0_1da/1 +TGTATATGTGTGTGTGTGTTTGTATGTGCATATGTGAAAGAGAGTGTGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_19217196_19217734_0:0:0_1:0:0_1db/1 +ACTCAAGTGTATCAATGTATAAAGCTAGTACGTGAACCCTACACACACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_4075909_4076300_0:0:0_1:0:0_1dc/1 +ACTATGTTCATAGCAGCCTTATTTATAATAGCCAGAAGCTGGAAAGAACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_186978576_186979074_1:0:0_0:0:0_1dd/1 +CTGCAAATCGGGTGTTTGGATTGGATTGATGGTTCAGTGGTTAAGAGCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_112188833_112189331_0:0:0_1:0:0_1de/1 +CAATTAATATTTATGAAAATTCATATTTATATATTGAAATGTAGTAAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_173609986_173610514_0:0:0_0:0:0_1df/1 +ACAATCTGGGAGGTGAGTTGGCTCAGTGCCCTGACTGAAGTGACAAGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_22017871_22018438_0:0:0_2:0:0_1e0/1 +CCCCTAGCTTTCAAGTCTTGGGGTTGAATCCACTGTCTCCTGCGTGAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_48541209_48541729_1:0:0_2:0:0_1e1/1 +GGTCTGCAAACATAACTGAGTATCATTAATATTGTCAAGGACAGGTTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_10384181_10384617_2:0:0_0:0:0_1e2/1 +TTCCTGTTGTTTTTGTTGTTAAAGTTGGCATTCTGTTCTTGTGGCTGTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_20392227_20392827_2:0:0_0:0:0_1e3/1 +CACCAAGAGAAAACTTGTTCAGATACATTGATTTTTAGTAAGGATATGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_171278949_171279483_0:0:0_0:0:0_1e4/1 +TCCAAGCTGAACAAACCCACCGGTCCATATTGCTGGGGCTGCTGCTGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_58815142_58815652_3:0:0_0:0:0_1e5/1 +GGAGGAAGACATCCATGTAAAGGAGCAAAATTAAAGATGGGAATTGTTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_157206264_157206747_1:0:0_3:0:0_1e6/1 +CATCCCCTAGTAAGAGTTATGATAAAATTACACTAAAGCTAGTTTTTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_130727486_130727887_0:0:0_1:0:0_1e7/1 +GGCAGGGTTTGGATATCTTTTCCCTACTGAGCAAGACAACAGCTTTGTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_56227774_56228368_1:0:0_2:0:0_1e8/1 +GAGGGCTTAGTGTTGATAACAACACTCTGCTAGCTCATTGGATAGAAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_163976865_163977422_1:0:0_2:0:0_1e9/1 +CCCCCCCCCGACAGATAACATACAGAATAAAAACTTGAACATGCCACACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_75768405_75768873_1:0:0_0:0:0_1ea/1 +AAACTGGGCTCAAGGATACCATGCGTTGCTTTATACCAACTTGGACCTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_99777250_99777759_1:0:0_0:0:0_1eb/1 +TCAACTCTAGAGTCCTTCCTAAAAAAAGAAAATGAAAAAAAAAAAAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_6944229_6944786_1:0:0_3:0:0_1ec/1 +GATCTAAAATTACCTAGAACATTACATGGAGATGTTGATTAAAGTCATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_6751099_6751639_3:0:0_0:0:0_1ed/1 +ATCCAAATAACTGTTCTCTTTCCATCATATGATACTGACACAGTGATCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_28492407_28492923_0:0:0_2:0:0_1ee/1 +TCTTAGAATGCTATGATTTCACATATCTCTGTATGTTGTAGTAGAAGAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_25977449_25977911_3:0:0_0:0:0_1ef/1 +CAATACAATAATAATGTATCATTATAACAGTAGACAAAAGAAAGGAATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_180012197_180012695_1:0:0_3:0:0_1f0/1 +GAGAACCGTGACTAATATAGAAGTTGGTACCAGGATAGGTTCTAGAGTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_139551031_139551593_1:0:0_0:0:0_1f1/1 +CATCAAGTCAAATTATAGCATTTTTAAAAAGAAACTTGATAGTATATGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_88565594_88566005_0:0:0_1:0:0_1f2/1 +TGTTCAGGCTAGAGTACCTGCATTAGCTCTTCCTTTCTCACACACACTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_28334498_28334996_0:0:0_0:0:0_1f3/1 +AGAGCTCCCTGAGACTAAACCACAATCAAAGAAATCACATGGTGGGACTC ++ +22222222222222222222222222222222222222222222222222 diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in6.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in6.fastq new file mode 100644 index 00000000000..094a63da07d --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in6.fastq @@ -0,0 +1,2000 @@ +@chr1_177668195_177668687_1:0:0_2:0:0_0/2 +GGCTGTTCTGTAACTCACTATGTAGACCAGGCTGGTATTCAACTCACAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_102240227_102240757_1:0:0_0:0:0_1/2 +ATTGGGAGCCCTATGATCCATCCATTAGCTGACTGTGAGCATCCACTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_135092709_135093083_1:0:0_0:0:0_2/2 +TGTGTACTTGGTAGCAGACAAAGCTGAACTAGACCGTGGCATTAATTCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_173363751_173364238_0:0:0_1:0:0_3/2 +AGTTTCTTTTCCTTGTTATAGCTGTAAGGGATCTGTCTGTTTTTATCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_155990043_155990565_1:0:0_0:0:0_4/2 +CTTTCTATTTTTCTCAAATTAATTACAATCAAAAGTACTTCTGTAACGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_3703883_3704401_0:0:0_1:0:0_5/2 +CCAAGAAGTGGGAGTGGGTGGGTAGAGGAGTGGGAGGGAGGGTATGCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_148211558_148212105_1:0:0_2:0:0_6/2 +TGCCACACTGTTAAAGACATTTATCTTCCCTCTTGAACACCAATCCCTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_30961675_30962138_2:0:0_0:0:0_7/2 +TTTCTGGTCCAGTCTATTTGGTTTTGTGTAGGCTTCTTGTATGATCATGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_86070681_86071151_1:0:0_0:0:0_8/2 +GTTTTATGATATCTTTACATATCCCATCTTTTAAAGTAGCCCTTCTATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_78259267_78259767_0:0:0_1:0:0_9/2 +AACAAAATCTGATGCACTTTTCTGGAGTATCTGAGGACAGCTACAGTGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_143451378_143451824_2:0:0_1:0:0_a/2 +TTGATAAAAACTTCATGGTACTGGTATAGAGACATACAAGTAGACCAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_163539961_163540475_1:0:0_1:0:0_b/2 +GAGGATGAATGAGTGACTTGAATTGGTGATTTTGAGGTCAAAATGTTTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_70390520_70391012_0:0:0_1:0:0_c/2 +AATTTTAAACATCTTATTAACTGAGATCAAAGATATTGATTTTCTATTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_119090463_119090959_0:0:0_0:0:0_d/2 +AAATGTTCACTTTGAAATCACTTCAGACCTACAGGAAAGTTACAAAGATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_12587911_12588392_1:0:0_2:0:0_e/2 +ATAATTTCACCTTTTGTCTCTGGGCGCTCATAAAAGATGCTATTGAAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_21875665_21876102_0:0:0_1:0:0_f/2 +GGGGCAGAAGACCATGCCACATGAAAGGACCACTTACAGAGCTAGTTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_22900274_22900767_0:0:0_0:0:0_10/2 +AATATATTTTAAAAATTCCCCATTGTGGTAGTGTAGACATAGGTCAGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_97511239_97511754_1:0:0_0:0:0_11/2 +TGCACTAAATAAAGATAGAATATTAAAAGCAGTAAGGGAAGAAAGGTCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_64669865_64670428_2:0:0_2:0:0_12/2 +CTTCTGGTTTTTCTGGCTTTCTACCCCGCAGAAAGTGATTTAGACTACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_69102786_69103213_3:0:0_1:0:0_13/2 +ATTTAAATTACACAAAATGAATATTCGAAAAAAGGTACCAAGTTAGTTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_117742994_117743506_1:0:0_4:0:0_14/2 +ACAGTCCAGTCTTCACTGACTGCTCCCCATCCCCTACCTCCTCCCCTCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_53703453_53703930_0:0:0_1:0:0_15/2 +TTCAACAGAAACCTTTCAGCACGGCTCATGCTTGGGTTGGTTATGTAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_17968135_17968661_2:0:0_0:0:0_16/2 +TAAATACAATACATGTTTGATTATGTGTGACTATTATCCATTAAATAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_126734590_126735074_2:0:0_1:0:0_17/2 +GGGCAAATGCTTAATTCTTTTGCTCTTCTCGTTTGAAGTTCTTATTGAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_15473022_15473574_0:0:0_2:0:0_18/2 +TCCTTCTAATTTCACGTTTTCTTTTTGTTTATAACACAGTGAGTTTCCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_32809503_32810008_3:0:0_4:0:0_19/2 +CAGGCAAGGCAACTGGAGCTGGAAGTTTAAACCTGCATGTTCATATTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_101160086_101160574_0:0:0_2:0:0_1a/2 +AGCATTGGAAATGTAAATGAAGAAAATACCTAATCAAAAAATTTAAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_86845143_86845638_2:0:0_0:0:0_1b/2 +GGCTTTCCTTGTGGCACTGTCCAATGTCCCTTTAAGGCAAAAGCATGAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_156394447_156394901_0:1:0_1:0:0_1c/2 +TTATGGCGAGATGAGCATCTCACTATAGAAATTAAAACTAATCAAAAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_175220096_175220545_0:0:0_1:0:0_1d/2 +TCTCATTCAATAGCCTAGACTATTACTTTAAATACAATAAAATTTAATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_66136304_66136892_1:0:0_0:0:0_1e/2 +AAATGGTTTTAGAAGTCCTTATCCTGGGCTTGGATCTTCTCATACCTCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_56699450_56700040_1:0:0_0:0:0_1f/2 +TCTTTTAAGTTGACAACTGAGTCTGAGCAGTGATGTTCAATGTATACTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_60449644_60450153_0:0:0_0:0:0_20/2 +GGGAACAGTAGCAGGAACAAGAGGGGTGGGGACAGATGCAGAAGTAGCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_28286517_28287074_0:0:0_0:0:0_21/2 +CAATTTTTCTCAGCTTCTGACCAAATTGCTCTGCTTGGCCTCATACTAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_127946423_127946897_1:0:0_1:0:0_22/2 +AATCCTCTTTGTGTAAGAACAGCTGGTGCTGTTAACTTGTCATCTCTCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_136274524_136275031_0:0:0_3:0:0_23/2 +GAGGGTGACTTGCTGAAGTCATTTCTCTCCTTTCACCATGTGGGTCCCCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_122372156_122372666_1:0:0_1:0:0_24/2 +GTTTCTGTGTGTCTGTATGTCTGTGAATGTGTGTGTGAGATTTTGTCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_19553027_19553520_1:0:0_0:0:0_25/2 +TTTGCGTATGGTGAAGTATGGGAGCCTTCTTACAACTGAAGAGGTGGTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_57071218_57071658_1:0:0_0:0:0_26/2 +CTGTGACTTGGTAAACTCCATGGGGTATCTCCGTACAAGGTGAATGACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_7557012_7557560_0:0:0_2:1:0_27/2 +CAGATTTCCTGACAGTCAAGCTGCCTCTGCATCCCTGAGATCATGCTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_18791508_18791966_0:0:0_0:0:0_28/2 +AAGCCAGAGTACGACTGCCCTTACATGAGCCCCATTCCCAATGAGCTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_56244256_56244708_0:0:0_0:0:0_29/2 +ATGTTTCCATTTGCATTTAGCTAAAAATTGGCAAGAAGATTGTCATCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_30613322_30613773_2:0:0_1:0:0_2a/2 +GATTGCTTCCAGCTTCTCTCCAATTACTTAGATGTTGGCTACTGGTTTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_161898116_161898586_1:0:0_1:0:0_2b/2 +CACTAATTGAGAAATGCCTTACAGCTGGATCTCATGTAGGCATTTGCCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_3742828_3743343_1:0:0_0:0:0_2c/2 +GTCTGGGAAGAACCCAACTGTGTTCTATTTAATCCTGCCCTCCTTCTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_59624032_59624611_1:0:0_0:0:0_2d/2 +ATTTATTTATTTATTTATTTATTTATTTATTACACTGTAGCTGTCCTCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_98734890_98735381_1:0:0_2:0:0_2e/2 +AGTAGACACAGTGATTGTACAACAGGACATCTGATGGGACATTAGGACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_170863521_170863976_0:0:0_1:0:0_2f/2 +GTTTTGATTGTAGCCTTCTTCTTCACTTGTAGATGACTGCTTTCTTGCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_111611961_111612483_3:0:0_0:0:0_30/2 +CCCACCTGGGACAGACTAAATGATGCTTAGTTAACTCTAAAATTTCTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_125730124_125730581_1:0:0_1:1:0_31/2 +ATCGTTCCCACATCTTGCTTTCTTATTCCTCACACCCACAACCACAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_10873266_10873801_1:0:0_1:0:0_32/2 +TTCACTGTAGTTGTAACAAATGAGTTGTTTGTTGTGTTTTATAAAAACAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_175631956_175632547_3:0:0_1:0:0_33/2 +GCCGAGGATGCTATTTAAACATACAAGGTGTCTCATATGAGACTGGGTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_20372115_20372592_0:0:0_2:0:0_34/2 +TGTCCTTCTTACCAGAATGGACAGATTGTGGAAACAGAAACATCTATGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_172022589_172023145_0:0:0_2:0:0_35/2 +GCCAGGAAAGAGGAGGAAAAAAATAGTCTGACAATACTGCCCCAGCCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_168140019_168140474_0:0:0_1:0:0_36/2 +AGGGATCTGCACAAGTTTGCAGGTGTCTAAGTAGGTCAGAGGTATCAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_12207936_12208461_1:0:0_0:0:0_37/2 +TCATCTCAGACTTGCTATTACAATATCTAATCTTATCTTCTGATAATTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_73438005_73438553_2:0:0_0:0:0_38/2 +TGGCGTGGAGGAAACACTGGTCTCCGTGGACGTCATTTGGCAGTTTTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_152770828_152771350_1:0:0_1:0:0_39/2 +CAGCTACAAGGAGGCACCCGGTCTCTAAAACAGCAAACCAACAAAGAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_23377131_23377643_1:0:0_1:0:0_3a/2 +ATTTTGTTTTTTTTTTAATCAACGGTAAATACACTGTGCATTATACCCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_101774130_101774651_1:0:0_0:0:0_3b/2 +GATCCAACAAAGATAGAGAACTTCAGACCAATTTCTCTTATGAATATCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_44505664_44506178_2:0:0_1:0:0_3c/2 +GCTGAGGGCCTGATTTTGCCTACTTTTGGACCCATAGGAACAATTTTGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_136585250_136585783_0:0:0_0:0:0_3d/2 +CTCAGATTGTCAGGTTTGTGGGACAAGTATTTTTTTTACCCACTGAGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_125479421_125479942_1:0:0_1:0:0_3e/2 +GACAGGATAGAGGCAGCTAGTAAGCCATGAGGGCAGAGCTTGGGGGCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_48288718_48289238_0:0:0_2:0:0_3f/2 +AAAAGATATAGACTAACAGACTGGCTAGACAAACAGGACGCAACATTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_162596088_162596584_0:0:0_1:0:0_40/2 +CAGGACAGCCACGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_114964476_114965085_0:0:0_0:0:0_41/2 +ACTCACCATTTTAGTGAGTATACAAGACAAAAACTTGAATAGTCTAATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_132214583_132215104_0:0:0_1:0:0_42/2 +ATGGTGCCAGGGATCCAAACTCATGTTCTTATGTTTGCACAACCTTCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_4422836_4423410_1:0:0_1:0:0_43/2 +TTTTATCACCACAAATATAAGTGGGCCAGTGAGAATGATCAATCCATTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72831428_72831958_1:0:0_0:0:0_44/2 +AACAACAAAAAAAAAAAACCTGGGCTAGCAAGATGGCTCAGTAGGTAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_17626572_17627059_2:0:0_0:0:0_45/2 +TTGAGGGAACACACATAGTAACCACCTACAGATAGGATAATTGGAAAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_122621502_122622050_0:0:0_1:0:0_46/2 +TAAACTAATTAATTATAATTTGAGGACAGGAGGGAATTACAGAACATACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_157981625_157982140_2:0:0_1:0:0_47/2 +GACGTCCTACATCCCTTCCAGGCTCAGCTGTTGGTTTTCCCTAGTTACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_86952334_86952916_0:0:0_1:0:0_48/2 +ATTTTGTCCTTCTCAATTTTTTTTCCTTTCTTTGGCTTTAACCTTGCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_56589802_56590323_0:0:0_5:0:0_49/2 +CATTACGTGACGGCATTACCCCACAGTACCCACTTTGCTATGCTATTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_44959275_44959852_2:0:0_0:0:0_4a/2 +GGGCACCTGTCCTCCGGTCCAGACGGTGGCTGGCTGTCCCCTGCCCACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_78655270_78655764_0:0:0_1:0:0_4b/2 +ATTATAGGTGCTTAGTGGGAAGCTTGATGACCTGAGTTCACCATGGGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_92742731_92743276_3:0:0_1:1:0_4c/2 +TGGGATGCTGAGGTGGGCGGGTATAAGGCAATGGAACTGGTCCATGGGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_133350357_133350894_2:0:0_0:0:0_4d/2 +GAGAGCGAGAGAAGGTAGAGAAGTAGAAGCCAGTCATTGCCATGCAGAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_18383798_18384307_2:0:0_0:0:0_4e/2 +AGGGGGAAAGCCTGTGCTTTTTATTAAAGCATACCTACTGGCTTAGTGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_94539200_94539737_1:0:0_1:0:0_4f/2 +AGTTTCAGCGAGAGACAGATAGATGAATGGAATAGAATTGAAGACCCAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_131360576_131361118_1:1:0_0:0:0_50/2 +CGTTCCTTCCTACCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_55802170_55802665_0:0:0_1:0:0_51/2 +GAAATACTGCTTTCTCGAGCCTATTAATTATCTTGATATGAACTGAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_160986523_160987031_0:0:0_1:0:0_52/2 +TTGCATTACAAGTGTGAGCCTCTGCATCTGCTTCGCCTACTGTGCGCAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_10207724_10208191_1:0:0_1:0:0_53/2 +CCTGTTAATGGCCACCAGATGGGAGAGGTTCTGAAGAGATTTCCTTCCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_186877031_186877586_1:0:0_0:0:0_54/2 +TCTTGCGCGCGCTCGACTGGGAAGGAAGAACGACGCTGCAACAGGATCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_76761957_76762468_0:0:0_4:0:0_55/2 +TGTTTATAATAGCGAGACGCTTGAAAGAACCCAGCTGCCCCTCAACAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_117599116_117599626_3:0:0_1:0:0_56/2 +TGGCAACAGCAACAGTGAGTGTCTGTGGTGGCTGCATCTGGGATGGACCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_174656805_174657230_0:0:0_2:0:0_57/2 +ACCACACTGTGATTCACAAAGCTAGGAAGCGCTCTCTTAAGTTCTCCCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_31215276_31215715_1:0:0_3:0:0_58/2 +AATGCCTTCCTGGGACTCTGACCAATGGAGCTAATTCCAAAGACCATACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_126165616_126166084_1:0:0_0:0:0_59/2 +AGGATGAAGATTATATGTGAAAGAAGCACTTTGGTAGAGGAAGACTGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_164029809_164030262_1:0:0_2:0:0_5a/2 +TGTTGGGGTGTGGATAAAGTGTATATGAGTTGAAAGGTTGATTTGGTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_121717872_121718374_3:0:0_3:0:0_5b/2 +TATTCTCATGCAATAAACACAAAGCAAATGAAGCCAAAGCTGATGCTCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_160410719_160411215_0:0:0_1:0:0_5c/2 +AGTGTGCTTTTTGTACAAAATCAACAAATGATTTTAATATGATAGTATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_100203985_100204499_0:0:0_1:0:0_5d/2 +GAAAGTCTTAGTTCCCATGTCTTACCAGCAGTCTAACTTGCCTTCTTGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_177503365_177503816_3:0:0_0:0:0_5e/2 +ACAAGAGGTATGTCTTGGTCTGCCTTACACTGTTTACTTAAGCTGCATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_164919242_164919704_1:0:0_1:0:0_5f/2 +CCCAAGCGGAGTAGACGGCAGGAAATAATCAAACTCAGGGGTGAAATCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_36958484_36958940_1:0:0_2:0:0_60/2 +ACCTTAGCCTCCTCCGAGCCGAAAGCCGCAAAGCAACTATTGTCTTTTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_99520185_99520697_2:0:0_2:0:0_61/2 +CGACCTGTGATGGTTTGTATATCCTTGGCCCAGGGAGTGGCACCATCTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_92584393_92584910_1:0:0_1:0:0_62/2 +AGCTACTGCTCTAACACTATATCTGTCTGCTTCCTGGCATGAAAATCGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_6665937_6666494_1:0:0_2:0:0_63/2 +TAATAATGATGTCAGCATTTCTTTCAGTGCCTCTAGGCCCTCTCTGACCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_103781308_103781731_2:0:0_0:0:0_64/2 +ATATGTATCAAAGACAACTCGTCCCAAAAGAACCTTTCTAGTCCTCTGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_35981688_35982179_0:0:0_1:0:0_65/2 +CCCTTCCTTGCTTCCTTCTGAAGAACCAGCTTGCCTCCATTTTAGGCTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_76873892_76874342_1:0:0_1:0:0_66/2 +TTCTGTAAGGCTGTGAATCACCCAATTTCTACATGTTTTCAGACCATGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_148924276_148924708_1:0:0_0:0:0_67/2 +ACAAACCGTAGATCAACTTTATTACCTCCTTTATTATATTTAGAGGTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_48352388_48352886_0:0:0_0:0:0_68/2 +AACATTTTACTATACCATTCAACCATCATTTGAGAAGTTTCCTCCTGCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_135109139_135109668_0:0:0_0:0:0_69/2 +CTGGCCAATGGAGATGCAGCCTATTGTCACAGACATGGTGACAGTGCACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_133271389_133271883_0:0:0_0:0:0_6a/2 +CTAACCAAGTTACCCCGAGAAGGGCTGTGCTCTGGAGCGGGGAACTTGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_143528403_143528953_0:0:0_3:0:0_6b/2 +AGTTTTATGAAACTCAGGTCAGCGATCCACACAGCACTTATCACAAGGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_60739061_60739616_3:0:0_1:0:0_6c/2 +TTAAGGAATAGTGATTTTTGTTTCCTGTTATTTTTGTTATTAGAGGTGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_86239673_86240187_2:0:0_0:0:0_6d/2 +ATGCGTGATTCTAAGGCTGGGCCGCTTGTCCTGAACTGTGTGTGCTGCGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_8425683_8426176_2:0:0_1:0:0_6e/2 +CTTGCTGTGTTTTCGTAGTCTTATACTTTGTGGGAACTAATCCACTGTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_34934564_34935093_3:0:0_0:0:0_6f/2 +ATTTATTCATGTATGCTTGAGTATTCATGTAGTAAAGAGAAGACAGCCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_43897170_43897709_4:0:0_1:0:0_70/2 +GATAAGGTCACAGTCTGTCAGTGATGCACAGGACAAATCCAAAACCCGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_64512455_64512956_0:0:0_0:0:0_71/2 +AAAGTCAGGAGAGGCTGAAAGCTAGGCCTCTTGTACCAAGCCACTAAGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72637152_72637620_2:0:0_2:0:0_72/2 +ATGCCAGTGCACTAACACAAAGCCTGGCATGGTAAGGGACATGCTCGTCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_149528405_149528902_2:0:0_0:0:0_73/2 +GTGAAATGATAGACACCAACCCGCTTAAAAAAACTTTCCACCCCAAATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_89951120_89951611_2:0:0_1:0:0_74/2 +CCTCGAGGTCGACTCCTCTAGCCCTGCATGGGATATGAGTCGTCCCCAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_108291981_108292457_1:0:0_1:0:0_75/2 +TTTTGGTTTGTTGAGGGATTACTTTCTTGATTGTTCTAGGGCGTGATTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130354891_130355474_0:1:0_0:0:0_76/2 +GATGTGCACAAACATAAAAAACACACACACATGCACACACAAAAAAAGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_166207187_166207634_1:0:0_3:1:0_77/2 +CTGAAGTCAGGCCTGGAACTCAAGCAGGACAGGATGCAGGCACAGATGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_178111549_178112035_3:0:0_3:0:0_78/2 +TGGACACAAAACATTGAGAATGAGATTGCAACAGGATTCTGTACTACAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_64705135_64705653_1:0:0_3:0:0_79/2 +AATGTACAGTGGGCTTGATATGAAAATATTACAACATATAATTAGATCGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_50237028_50237524_0:0:0_2:0:0_7a/2 +TGCAGCTTCTGGGTATTATAAATAAGCCTGCTATGAACATAGTGGAGAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_134752385_134752911_2:0:0_0:0:0_7b/2 +CATTCTCTCCTTTGTCTGGCAGTGCCACAGCACAGGGTGCCGTGAGAGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_168207741_168208312_2:0:0_0:0:0_7c/2 +GAATGACCCGAGATGTGAGGACTAGGCAGGTTGCTGGGAGGAGGCCATGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_151034392_151034882_0:0:0_0:0:0_7d/2 +ATTAAAGACTTTACAAAAACTAACCTCATGAAACTGAAAAGCTTCTGTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_149618965_149619431_0:0:0_1:0:0_7e/2 +TTAGGTCCCAACACTCACTAAAAAGACAAGGTTTTCCCGCCGTTCTCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_72479618_72480144_1:1:0_0:0:0_7f/2 +GGTGCCAACCACTGTCAAGCTAATAGCAGACTAAAAGTTTTACCGGAGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_18771436_18771929_1:0:0_2:0:0_80/2 +TAGTTTTCCAGTGAGGGCTAATAGAACAAAGTGGTATAAATGGTTCAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_177626454_177626877_2:0:0_1:0:0_81/2 +GGTGGTGCAAAGAGAGTCCTGAAGCTGCAGATAGAGTGACAAGAGAAGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_58671914_58672334_4:0:0_0:0:0_82/2 +ATTCTTGTGTGACCACGCCCCTAGGATCCTGGGATCCTGGGTGTGTTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_123634655_123635138_1:0:0_1:0:0_83/2 +TCATCCAGAGGTCTGGAATCTTGTTCACAGCACCCATATCTAGCAGCCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_32777949_32778514_0:0:0_2:0:0_84/2 +ATTTCCAAAAATTAAACTTGATCTTCATATTAACTTTCTAATCTACAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_38321026_38321532_2:0:0_2:0:0_85/2 +TTGCTTACATTCATGGTAGGCCTAACACCACCCAGCATCCTTTGCTTCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_31837668_31838221_1:0:0_2:0:0_86/2 +CCTGGTGTCATTAGCAGAGCCTGGTGGTTTCTGGATTTAACTGGCATTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_189752778_189753180_2:0:0_0:0:0_87/2 +AAGAGAGAGAGAGAGAGATAGCGAGAGAGAGAGAGAGAAAGACAGACAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_43602264_43602720_2:0:0_0:0:0_88/2 +TTGTCTTGAGCTGATGATGACATGAGACATTATCCATCTCCAAAATGCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_29558267_29558774_2:0:0_0:0:0_89/2 +AATTAGAAAGGGCAATCTGCAAATTCATGTGGAATAACAAAAAACCTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_59048796_59049203_1:0:0_0:0:0_8a/2 +TCTGGAACTATAGGACTAAACTTGATTGGCTGATGCTAGGGAGCAGCTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_31285666_31286194_0:0:0_1:0:0_8b/2 +AAACAAAACAAAACAAAACAGATTCAATCATGTTAAGAGGGATAACCTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_159055630_159056144_1:0:0_3:0:0_8c/2 +GCTCTCTCTAGGAAGGCTCCTTGTTGCCAGACGTCATCCTCTCATTCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_163934531_163935036_0:0:0_1:0:0_8d/2 +CAAAGGCTTACCTAAAACAAGCAGTATATGACAGCTAGCTGAAATAAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_116610918_116611481_1:0:0_0:0:0_8e/2 +ACTTAGAATTCTAAATAAAAGGTTAACTGTTTTCTTGGAATGCACTTAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_141208156_141208756_0:0:0_0:0:0_8f/2 +CTGAGTTATGCAGCCTTGCAGAAAGTTCTGGACAGGGTTACTTTTCAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_45492268_45492792_1:0:0_3:0:0_90/2 +AGTACATTAGCAGCCTCTGGAGAAAGAAGATATGCTGCAGTTTGGAAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_11755179_11755683_0:0:0_1:0:0_91/2 +GGGCTCCCACAAATATTCTAGTATGCTTTGCTCTAGGATAAATAGAATCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_156738022_156738530_2:0:0_2:0:0_92/2 +GATGCAGTATAAATGGTGTAGCAGATGCCCGAGACCTCAAACACACCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_95480426_95480839_0:0:0_0:0:0_93/2 +TTAAGTGATGTAACTGGATAACAGTAATGAAATTTTAGGTTCTCAGTGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_173460574_173461156_3:0:0_1:0:0_94/2 +TAAATACCAAAAAATGGATTTTGTCAAATAAGGTCTTATAATACCACATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_17445381_17445808_2:0:0_4:0:0_95/2 +TAGAAACTGGCAGCCTTTAATTGTCTTGTAGCTTTACCTCTTTGTATGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_76540003_76540477_2:0:0_2:0:0_96/2 +GTGTAGCTCATATGTGACAGCAAACATTGTCCTTGCTGTAACTTTTAGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_12896019_12896500_1:0:0_1:0:0_97/2 +ATCCCAGGAGCTTGGTCACACCAGGTTCTCAGGATCACAGAGGCAGCTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_41708628_41709145_0:0:0_1:0:0_98/2 +TACATGTGTGTATATGTGTGCATGGTGTGTACGGTGTGTATGTATGTGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_106826115_106826660_0:0:0_1:0:0_99/2 +TGTCTCATTTATGGGTCTTTAATTCTATTTTATTGATTGACATGTCTGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_13247654_13248181_1:0:0_0:0:0_9a/2 +ATCTGCAGACAGTTCTAACATCTGATGTTCATTTACTACAGACCAGTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117777350_117777861_0:0:0_1:0:0_9b/2 +AAATGTACTCACTGATAAGTGGATATTAACCCAGAAACTTAGTATAGCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_77191506_77192008_2:0:0_1:0:0_9c/2 +TAAAAAAAAAAACTCTTTAGTTTGGCTTGCATGTGATTCAAGGTTTCCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_36849743_36850269_1:0:0_1:0:0_9d/2 +TCTTTCTAGAACAGACTCCAGTTCAATAACCATTTATTGGTTGGGTGATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_148890840_148891366_0:0:0_0:0:0_9e/2 +AATCTAAAATTTGAACCCCTTATACCCTTCAAATCCACCATCAACTGTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_84671373_84671880_2:0:0_1:0:0_9f/2 +TTCTAGGGACATTCTTTTCTTTCTACAGATTTCGATAATTAAAGGAGAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_102434771_102435253_0:0:0_1:0:0_a0/2 +ACTTCCTCTTGGTTAGTTGTCCAGTGAGTTCTACATTGGTCTGTCTCTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_100209819_100210321_0:0:0_1:0:0_a1/2 +TCTAAATGGGATGTGGCTAAGCTGGCAGTTTGCTGGCTTAGCATTTATGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_62044005_62044573_2:0:0_1:0:0_a2/2 +GTCAGACATCAGCATCACAAATGCAGAATGACAGAAATTGACTTGCACCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_85132332_85132871_1:0:0_3:0:0_a3/2 +CAAAAGAAAACATTTAATTGGGGCTTTTTTACAGTTTCAAAAAATAGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_58843215_58843696_0:0:0_0:0:0_a4/2 +CGTGCCAGAAGAAGAGAGTGACTCCTCTGGAACTGGAGATACAGGCAGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_137975188_137975732_1:0:0_1:1:0_a5/2 +TGGCCAGATACAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_141967561_141968074_0:0:0_0:0:0_a6/2 +TCAACATATATGACATCCATAAATCAATGATTTGACTATGAAACCATGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_8624607_8625140_1:0:0_1:0:0_a7/2 +TTAACTTTCAAGACAAGTGAATACTATATGATTTGGTGATTCTATGCAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_138783244_138783650_1:0:0_1:0:0_a8/2 +GATACTCATGTGTGTGCCCAGCGGCTCTTTGAAGCTTACGTTCTTACATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_52699200_52699639_1:0:0_1:0:0_a9/2 +TCGCCACCGTCTGCTGTCACCTGAATTTTTGATCTTAGCCCTTCTGACTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_32849205_32849709_0:0:0_0:0:0_aa/2 +AAGTCAGAGGAAGCAGCCAGAATTAGCTGGAGCACCATGAGAAGCACCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_182043596_182044137_0:0:0_0:0:0_ab/2 +AAAGAAAAGAAAAGAAAAGAAAAGAAAAAATGGACAAGAAGGCAAATAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_136004325_136004842_4:0:0_0:0:0_ac/2 +AATCAGCTAGTTGGTTTGTCAGAGGAACTCTCAAGAGAAGATAGCACTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_174545541_174546018_2:0:0_1:0:0_ad/2 +TGTCTGAGGCATTCTGCAGAGCTGCGTTACTTTGTTTTGTTGAAAGGTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_11117502_11117925_0:0:0_1:0:0_ae/2 +CACTGCATATACTATTGACCTAGTCTGACATAATACCTCACTTTCCTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_44177515_44177974_0:0:0_3:0:0_af/2 +CTCAAGAAGAACTAAACCCACACAGAAGTACCTTGGTCAATATTTCACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72645507_72646002_0:0:0_0:0:0_b0/2 +AGCCCCAATGAAATATTTCATGATGTTTCTTTACAGGAATAGAAACCCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_147283777_147284272_0:0:0_1:0:0_b1/2 +TGCTCCCTTTTATTTTTGTTGTTAGAGTTGGGATTCTGTTCTTGTGGCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_133675964_133676447_1:0:0_0:0:0_b2/2 +CATGTCAATGTGTGGGTCTGTTTGTAGGTATGTGCCTGAGCGAGCAAGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_114568587_114569130_0:0:0_0:0:0_b3/2 +TCCGAGTTGGGGTTTACTATTCTTATTTGTTTAGTAAGATATTAAAGGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_111695385_111695895_0:0:0_0:0:0_b4/2 +TGATTTTCTCATCCGTAGATGAGTGGGCTTTTAACCTTGGCTTGGGTGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_172273320_172273788_1:0:0_0:0:0_b5/2 +AAGAAAACACTATTCCATAGGAACCTGAAGCCAGCTTCCCGTCTCAAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_29014340_29014871_0:0:0_2:0:0_b6/2 +GCAAGGCTCCATCTCCTACTAGCACCACTCCCTATGGGCCAAGTATTCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_177626521_177627066_1:1:0_0:0:0_b7/2 +GACCGGCACCTCTCACTGTGACCATTTTGAGTTTCTTGCTCTAAACTGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_110742845_110743354_1:0:0_0:0:0_b8/2 +CATCCAATAGATGACTGAGCATCCACTTCTGTATTTGCCAGGTACTGGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_14101155_14101687_3:0:0_0:0:0_b9/2 +CTAAGGTAAATTAGATCTTCCACCTTTGATTTACCCAGTTCTCCCAAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_38147934_38148475_0:0:0_0:0:0_ba/2 +TCCATCTGGAGTATTCAGAGGGCCCTTGAGGTTTGATGCTCATCCACGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_84834550_84834957_2:0:0_1:0:0_bb/2 +AGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGCTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_94046734_94047311_0:2:0_1:0:0_bc/2 +CTGTGGAACAGGAAGTCGAAAATTCTAATCAGGATTCTCTTGGTTAAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_138724568_138725155_1:0:0_2:0:0_bd/2 +GATCTTCCCTTGGCTCAGCATTATTAAGGAAGGTGCTGGCTGAACCAGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_105672406_105672966_0:0:0_1:0:0_be/2 +TCAATTACTACCATTTTGTGCATATTTTAAAAGCACACTATGGACACACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_157814995_157815529_0:0:0_3:0:0_bf/2 +TGACATACAAGTAATAAAGCCAAATACTTAAATAGGCCATCTCTGTTACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130059190_130059641_1:0:0_0:0:0_c0/2 +GTTGGGGGTTGGGGAAATCTTTAGGAAGTTCCAGAGACCTGAGACAGGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_18604367_18604942_1:0:0_0:0:0_c1/2 +TAGCGGTACACTGTGTGAGCTCTAGGAAAATACAGAGCTCAGGAGATTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_160029930_160030407_0:0:0_1:0:0_c2/2 +CAGATAGCTAGCTTATGGACTAAGATTTTTTTTTAGAGTGGCTTAGTACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_32417120_32417575_0:0:0_3:0:0_c3/2 +AGTTATACATGTTGTGGTGGACCCCAGCAACAAAATTACTTCCATTCCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_91572336_91572825_0:0:0_3:0:0_c4/2 +CACCTTCAGGAACTGTTAGAGGTGGTTCCTGTTGCTCTTACGCCCCCCGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_167308006_167308522_0:0:0_0:0:0_c5/2 +GCCCGATCGCCTACCTCACACTAGAACCCTGTCACACGGTGGCTGGACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_53658226_53658697_1:0:0_1:0:0_c6/2 +GTTCTTTTGTAATTGCGTTACCTCACTCAGGATAATGCCCTCCATGTCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_75542501_75543075_2:0:0_0:0:0_c7/2 +AAGTTCTCTCTCGCCAAGGTAGAAGCTAGAAAAATGCATATGTCCTGACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_49392954_49393517_0:0:0_2:0:0_c8/2 +GTATCTTTTTCTCTCCTTTTCATTTTTTAAAGTTTATTGTTGTTCTTAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_18890524_18891056_1:0:0_0:0:0_c9/2 +AGTTGATTCCGGACTCTTCAGAGTCCAGCTTTTTGGGGGTTTTGTTTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_13661516_13661931_1:0:0_1:0:0_ca/2 +AAAAGGAGTAGGCTAAGGTAGTGAATACACTCTACATCTCTATTGTGGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_69507936_69508419_2:0:0_1:0:0_cb/2 +CACCTCGAGAAAGAGCCAACCATAGAGCATGTGTGTTGATTGTTTAACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_171186227_171186672_2:0:0_1:0:0_cc/2 +CCCTTCTCTCTTCTAGAAACCAGACAATCCGTCCTTATACTCTCTAGTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_151167139_151167658_0:0:0_3:0:0_cd/2 +TCCAAATTAGACAGACTTCCTCTTCCTGTGGCCTGGACTGTTTTTTCTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_166490443_166490901_1:0:0_2:0:0_ce/2 +GATGTCAGAAACATGATAGGTCTCAGAATGTGAGGATTTTAATCCCAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_78053476_78053981_1:0:0_0:0:0_cf/2 +ATAGCATATCCCCTTAGCCAGAGAGCTTAGACTGGAGAAGCACAGCTGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_27573317_27573793_0:0:0_2:0:0_d0/2 +TTTAAGCTTATATAATAAAAAACATAATTACAAATCTATACAAAAGTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_74520986_74521432_1:0:0_4:0:0_d1/2 +TTTCCTTATAAAGTCTGAGAGTTTAGTTAGTGCTGACTTGTCAGAAACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_194568812_194569255_1:0:0_0:0:0_d2/2 +AAGTACCATCTGTATTAATGATTCACAGTTATTTAAATATTTGAACAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_173094678_173095086_1:0:0_0:0:0_d3/2 +TAAGGTTGAGTTTCTGATAGGATACCATGAGGTAAAGATTTCCAAGCAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_125473775_125474200_1:0:0_0:0:0_d4/2 +GCAGCTTGACTCCGGTTGTGATTAATCAAAAGAGGTGACCCTGGGAGACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_60312834_60313394_2:0:0_1:0:0_d5/2 +GAAGGAACGGGAAGGAGAAATGGTGTAATTAAATTATAATCTCAAAAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_21769340_21769783_1:0:0_1:0:0_d6/2 +GGCTAAGATCAAAACTTCAGGTGACCGCAGATGCTGGCGAGGATGTGGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_29011734_29012196_0:0:0_0:0:0_d7/2 +AATCAGATTTTGTGTTTTGTTTGGTTTTCCATTAATGCTTTCACAACGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_55988735_55989188_1:0:0_0:0:0_d8/2 +AAGATTAGTTCTAAAGACATTACAGCTGCCACTCCAAGTTCTTGCCCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_143689772_143690244_0:0:0_2:0:0_d9/2 +TCTAGTTAATTAACACTGTTATTACTTTACATGTTGCTCCATTTTGTGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_102292799_102293241_0:0:0_2:0:0_da/2 +GAATACGATTACTAATTCGTTGAGAAGGTGATATGGCCATTCACAAAACG ++ +22222222222222222222222222222222222222222222222222 +@chr1_175815890_175816392_0:0:0_1:0:0_db/2 +AACATTTCAACCTCTCCATGGCACTGAAGTTTTAATCAGCCAATCAGGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_65030887_65031423_1:0:0_0:0:0_dc/2 +TAATGTTATTCCTGAGATTTTTCCAGAGAAACAAATCCCACCATTTTTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_77446136_77446727_1:0:0_0:0:0_dd/2 +GGACTACTTTCACTAAAGTGGAAAAACTCAATGGTGCTGTGAAACCTCGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_79825884_79826306_1:0:0_0:0:0_de/2 +CAGGGGAACACCAGGGCCAAAAAGGGGGAGTGGGTGGGCAGGGGAGTGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_142137580_142138145_0:0:0_1:0:0_df/2 +GCCTCTAACAGTACCAAGGCTAAGCTGTTCACTATGACTTCATACCTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_77524851_77525306_1:0:0_2:0:0_e0/2 +GCAAGCTCCCGAAATCACAAGTTTGCAGACCAGGCAATGGGAAATTAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26694201_26694676_0:0:0_0:0:0_e1/2 +ACAATCGAATCATTATCTAGATATTTTGATTATCTTTGCTTTAGGTTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_93157579_93158060_0:0:0_1:0:0_e2/2 +CCTTTGGGATTCTCCATCCAATGAGCCTCAGTTTCCTTACGAGAGGGGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_93554302_93554745_0:0:0_1:0:0_e3/2 +ACAGGATGCAGCTGGAGACTTCAACACCTTACCTCCAATAATAGTCATAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_115859373_115859816_1:0:0_1:0:0_e4/2 +GCATGCATCAAAGCAATGGTCCCTTAAAGCAGAGGAGTCAAGACTTTTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_59908209_59908731_3:0:0_0:0:0_e5/2 +CTTGTTGTCTAAAAGGACTGAAAGGCAAGATTGGCTGCTGAGGTACTTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_154628329_154628794_2:0:0_1:0:0_e6/2 +TGTACAGACACTTTATAGGTGTCTTTGGTGACTTTGGTGACACTCTGGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_38934187_38934653_1:0:0_1:0:1_e7/2 +TTATAGCTTGCAATAGAAAATGGAGTTTTGTTTTTGCCAAATAAATGGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_176440703_176441215_3:0:0_1:0:0_e8/2 +GGACCGAGCCAGTCTAGATATTGCAGAACTAAGAGTGTGTCTGTGAGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_146248574_146249007_1:0:0_0:0:0_e9/2 +GAATAGATTGTACAGAATCAATAACCTACCAAGCATTTGCCTAGGGACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_137417062_137417534_1:0:0_0:0:0_ea/2 +ATGCCCAGTCACCCACAGTTGGTCTCCTGTCTCAGCCCCAATAACTAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_55607180_55607772_1:0:0_0:0:0_eb/2 +GGCACATCATTATCCATTGGTAAGCTTTGCTTTTTCCACAAGGTCACTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_174928179_174928755_0:0:0_1:0:0_ec/2 +AATTGCAAATAATTTTTATCCCATTTTGTATGTATGATAACTGATACCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_113923154_113923648_3:0:0_1:0:0_ed/2 +TAATGTGAGGTTACCTCTGGCACTGAGGACTATTAAGTGGCTTTAAATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_78423064_78423594_1:0:0_0:0:0_ee/2 +AACTTGATATATGTTACTGTGGACCAAATGCCCTTCCTTCTCCAGTATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_154582561_154583019_0:0:0_1:0:0_ef/2 +CAGCAGCCTTGTTTGTAGTCTTATTATGAATTCAACAATATGTCACATCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_181723357_181723842_1:0:0_2:0:0_f0/2 +CATGGCCATTTTCAAGACTCAGGTTGTGGACATCACACTAAGTGAGATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_176206787_176207249_1:0:0_1:0:0_f1/2 +TGTGACAGTCTCTGGTGGCCTTACACTCCTCCTCTTTTTGCCTCTATGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_156026308_156026788_0:1:0_2:0:0_f2/2 +ATTTTATTTTCAAAGCACTAAATTATTAGAATATTTTACCTTTTTATATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_55128175_55128671_1:0:0_0:0:0_f3/2 +CAGAGCAGTGAGCGAGTTTCCTGGAGAGGCCCGTGAGGGGACAGTCACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_184447109_184447646_1:0:0_1:1:0_f4/2 +GTTATATAACCTCATAGCAGTCACCAAATGAAATAAGACATTCCTCGTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_194617734_194618226_0:0:0_0:0:0_f5/2 +GTGATTCTCACATTTATTCTTCCTCTATTATTGTTTATGTCTGCATGTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_80810218_80810755_0:0:0_0:0:0_f6/2 +AGAGAAAGGCAGAGAAATAGAAGAGAGAGAGAGACCTACCTCTGATAACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_144296368_144296930_2:0:0_2:0:0_f7/2 +ATAGTTCCTTTTGACATAGATCCTTCTAAAGGAATTGTAAGGGAATGTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_108312503_108312946_1:0:0_2:0:0_f8/2 +GTTAAACAAGCATGCAATCCCACCAACAATGTAGGAGTGTTCCCCTTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_78228179_78228640_0:1:0_0:0:0_f9/2 +CTGAGTCTTGTTTGAGGATGGATGAACTGATATAAACGTTTTCAAAAAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_52088998_52089426_1:0:0_1:0:0_fa/2 +CTGTCCTGTCTTCCCTCTCCTCCGATCCCTCTTCTGAGTACTGAGCTTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_30782403_30782942_1:0:0_0:0:0_fb/2 +AATATATTCACCTACACCTGTTAACTCAAAGGATCTGCTTCAATACTTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_6435675_6436268_3:0:0_2:0:0_fc/2 +GACTCATTCATTCCCAGAGAGGAACAAAGGAAAATACCACAGGCATTTCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_164237997_164238538_0:0:0_0:0:0_fd/2 +CATCAGACAGACTTCCAGATAAAACGGGTTTCAGATGAGATCAGTACTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_187097969_187098475_2:0:0_2:0:0_fe/2 +CCATAGCAGCTGTGTGGAAGTCATGACTCCTGGAGGTCAAGTGACTATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44694856_44695375_3:0:0_1:1:0_ff/2 +TTCCATAATATCTCTTACTATCAATGGACTCAATTCGCCAATAAAAAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_111782668_111783223_1:0:0_3:0:0_100/2 +GCTCTATCCCGTGGATGGCTGTGAGCATCCCCTTCTATTTGTCAGGCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_94206847_94207360_1:0:0_1:0:0_101/2 +AAGCAAAACTGAGAAGCGGCAAGGAGGAGAGAACAGAATGGAACATCACG ++ +22222222222222222222222222222222222222222222222222 +@chr1_132119789_132120286_3:0:0_1:0:0_102/2 +GGCAGGTAGGCGGCGGGCGGACAGGCCGGGCAGCTCAGTGAACTCATATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_34226734_34227203_0:0:0_0:0:0_103/2 +AGCGGGCTACTGATAGCCCACAGGTTCAAACCAGACAAAATCACAGTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_138105716_138106319_4:0:0_1:0:0_104/2 +ATAAACAATCATGGCTCCTTAATTAACACAAATACTTTGAGGTCTCAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_126030856_126031342_1:0:0_2:0:0_105/2 +CAATTGTTGTAGAAACATTTCAAGAAAAGCGTGTATACAATTCACTAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_118807485_118808058_0:0:0_1:0:0_106/2 +TTCCGAAAAAGAAATAAGCAGAAAGCTGTTTGACTTTTCCTGGGGTGACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_19849114_19849606_2:0:0_0:0:0_107/2 +TTCCTTAGGGTGCTGTGGTGAAGGTCTTTTATGACAGCAAATGGCAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_66877733_66878136_2:0:0_1:0:0_108/2 +GAGCATCATAATGGCCCATCGGTATCAAAGCTAAGACACGAGCATGGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_132522495_132522987_0:0:0_1:0:0_109/2 +GCCCTGACTAGTGTAATAGGCCACAAGACGAAATGGAGCCTAGATTCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117050436_117050942_0:0:0_1:0:0_10a/2 +ACCCAATCACAAAAGAATACACATGATGCGCCCTCACTGATAATCGGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_125967212_125967705_0:0:0_0:0:0_10b/2 +TCAGGGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_69313718_69314189_1:0:0_2:0:0_10c/2 +TTTTCGTAGATGACACTATCACCTCTGCGTATCTGACCTCATCCTCAGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_60897368_60897871_1:0:0_1:0:0_10d/2 +TTCTCTAGCTTCTCCATTGGGGGCCCTGTGTTCCATCCTATAGATGGCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_174325015_174325549_0:1:0_2:0:0_10e/2 +TTAGAAATAACTTCAGAATGTCTTTTTGCCCCGTACAAATAAATAAGCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_85055965_85056468_2:0:0_0:0:0_10f/2 +CATAGAGAACATCGGCACAACAATCAAAGAAAATGGAAAATGCAAAAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_131415777_131416249_5:0:0_1:0:0_110/2 +TTTTGATCTCCTAACCAAAGGAAGATCTCCCAGTTTCATTGGTTCCAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_67136277_67136702_3:0:0_0:0:0_111/2 +GTGCCATTCTGCTTTACTCAAGTGTTCTCCGTTTTACAATTCAGGAAAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_8402131_8402528_1:0:0_2:0:0_112/2 +TAGTTCTTATTACCATTTGGTTGATTTCACCCCTGATTTTGATTATTTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_155126875_155127345_1:0:0_3:0:0_113/2 +TTGGCCAGCGTGAGATACATGCGACCCTGTTTAAAAAAAAAAAATCAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_93916438_93916928_0:0:0_0:0:0_114/2 +GGCAGTGATGTCTGAGGAGGACTCTTTGGGCAGATCTGAGGCCTGCTCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_135734641_135735118_0:0:0_0:0:0_115/2 +GTTGGGCAACCAGTTCATAGCACCACAGCTGTAGGAGGCAGAACTGGATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44391025_44391499_0:0:0_1:0:0_116/2 +TTAGCCAAATTAGAGGGTCGTCTTGAGGCACCTCAGAGACCAGAGTCTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_110722550_110723095_2:0:0_4:0:0_117/2 +ATATAGTAAAATATATCATTGTTTGTATCTAAGCCATTATATAGATACGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_185586471_185586808_1:0:0_0:0:0_118/2 +GCTTTCTGGTCTGATTTGACTCTTAGCGAAGGTAAATGTTCACGCACCGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_182936908_182937483_1:0:0_2:0:0_119/2 +CAAGCAGACACATTCATGAGGATTCTATCTGATTCTTCAACTTTTATTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_136882207_136882635_0:0:0_2:0:0_11a/2 +GTTTGGTATTTGAAAATAATGTCTGTGTAATGGATTATGAGAACGGACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_22027558_22028086_0:0:0_2:0:0_11b/2 +CCCTGGAAGCTCTGTGGAGTCTGGTTGGTTGATATTGTTGTTTTTCCTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_101069088_101069523_0:0:0_0:0:0_11c/2 +CTCCAGCTTGTTTCTTCAGACCTTTTGCTTGGAAAATTGTTTTCCAGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_133430180_133430643_0:0:0_3:0:0_11d/2 +CCTGAGATCCTGTCACTTGATCTGAAGTTTTGCCTTCTGTCTCCCCTGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_141505317_141505766_0:0:0_2:0:0_11e/2 +TTATATGCCCCAGTACAGGGGAACACCAGGGTCAAAAATTGGGAATGGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_103387516_103388014_1:0:0_1:0:0_11f/2 +ATGATTTCCCTACCTGATGAAGGCTTACTTCTTTCTTCACCTTATTTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_134753416_134753860_0:0:0_1:0:0_120/2 +GGACCTGGGCTTAGGGGACAGCAGCAGTCTGACCTCGGCAACAGGGAGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_168048225_168048764_3:0:0_0:0:0_121/2 +CTATCATGATCACATTACCCTTACATCACCATCATCACGAGCCCATCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_15110325_15110842_0:0:0_1:0:0_122/2 +TATGGTTGTATTAAAGTTGACTAATATTAAGAGCTTAAATAGATTTAAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_71511848_71512298_1:0:0_1:0:0_123/2 +GCTTATTAATCCTCTTCTCTTCTTGTATAAAGGGTGGGAAGTAGGTGAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_37275066_37275622_2:0:0_0:0:0_124/2 +GCTGGTTTCCAAATCACAGAGACCTCTCCTGCCTCTACTTCCTGAATCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_191970326_191970894_1:0:0_0:0:0_125/2 +TCGTTAAGAGTAACCAGGGCTCTTAACTGCTGAGCCATCTCTTAGACTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_137258018_137258449_1:0:0_1:0:0_126/2 +TATTGTGAAGTGTTATGTCTGATTGGCTTTTTCTCTTCTTCGGTGAGACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_163885263_163885763_1:0:0_0:0:0_127/2 +TGCAAACCCTTTCAGCTCCTTGGGTACATTCTCTAGCTCCTTCATTGGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_95122061_95122611_1:0:0_2:0:0_128/2 +ATCATCATAGGTGGGCAAAGGAAAGTGTGAAATAGTATAATTTCATGGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_191245641_191246131_1:0:0_1:0:0_129/2 +TTCTTGAGAGAGGCCAGGCTTTGGGGAACAGATGTCGCACAGCACTAAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_11721955_11722368_1:0:0_3:0:0_12a/2 +GGGTTGGAGATCCCTTTAGCTCCTTGGGTGGTTTCCCTAGCACCTCCATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_102954712_102955237_1:0:0_1:0:0_12b/2 +AAGTGGTGTAACCCAATCACAAAAGTACATACAGGATATACACTCACTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_26914346_26914925_0:0:0_1:0:0_12c/2 +AAGGGGAAAAAAAACCCTGCATCTGATATGCAAAGACCAGTCAGAATAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_151053369_151053909_1:0:0_0:0:0_12d/2 +TCTTCTGTCTTGAAAAAGAAAAAGAACACACCACACCCACACACCACACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_93621447_93621970_1:1:0_1:0:0_12e/2 +CATTAAGTGTTAGTTTTAATAGCGCATTGAAAACCCTACCATTTCAATAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_13530953_13531445_0:0:0_0:0:0_12f/2 +GAGTTCATTAGTACATTGGTTGTTTGGAACACAGAAAATCTTTCCCCATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_154530120_154530631_2:0:0_4:0:0_130/2 +AGGCTTTACTTAATCCAAAGCATAAGTACATTGTTTGACACCCTGCAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_100109085_100109588_0:0:0_2:0:0_131/2 +TCACAGAGGACACTCACAGAGATGAACCATGCTCCCAGGGACAAGATGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_150348101_150348543_0:0:0_0:0:0_132/2 +ATTAAACCTGCTGAGTTATTTGAATTCCAGAGACTTACATAATAAACTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_8725925_8726392_0:0:0_3:1:0_133/2 +TATTCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATCATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_189147844_189148204_2:0:0_1:0:0_134/2 +TTAAGACATATTAATTTTAGGAAGTAAAAATAAATTCATTTAAATTGGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_45618673_45619149_2:0:0_2:0:0_135/2 +CTGGATGTCGCTTGTGCAGATCTTGAAAATTTTGTCATAATTGCTGGGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_104062147_104062721_1:0:0_0:0:0_136/2 +ACAAAAACAAGTCAGATAAGGCAGTCCTCTGGTACATATATAAGAAGAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_138405158_138405766_1:1:0_1:0:0_137/2 +CAGGAGGAGCAGGGACGGTCTCTGACGCTGTTGCCTGCCTCTAGATCCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_115548969_115549503_0:0:0_1:0:0_138/2 +TACTCTGTTATCTATGCAGACCAGAGCCTAGCATAATTGTTCTCTGAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_195151172_195151687_0:0:0_0:0:1_139/2 +TTTATCAATACACTCAGCTTTCTAGGCAGAGATTTTTAGGATCAAATGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_138103424_138103925_0:0:0_0:0:0_13a/2 +TCTTAAGCAGCATGTTATTAGACAGAAGTAACAATAACATAAAAGTAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_84481564_84482032_1:0:0_0:0:0_13b/2 +CCCCAATCCCCCACCCACCGACTCCCCCTTTTTGGCCCTGGCATTCCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_180211651_180212100_2:0:0_1:0:0_13c/2 +AAAAGGACCCAGCCTGCTCCTGCATCCACTGACTTCCTACTTTGCGTTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_19484875_19485375_1:0:0_0:0:0_13d/2 +TGTCTCAGTAACTCCCTCCATGGGTATTTTGTTGACCATTCTAACAAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_8815773_8816268_0:0:0_1:0:0_13e/2 +TCAGATATTCTGAGAAGTTTGGGATTTCAGGCATGAAGTCCAGGAAAGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_118367902_118368405_1:0:0_0:0:0_13f/2 +GATTTCAGACTGTAAGTCATTTCAATAAAGTGTTTAATATAGAGAGACAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_83281820_83282310_2:0:0_3:0:0_140/2 +TGAGGGCTCTAAATCACAAATTCACTAGGATTAGACCAGACTAGTGCCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_24810903_24811377_2:0:0_0:0:0_141/2 +AATCGGATAGGGGACTAATATCCAATCTATATAAAGAACTGAAGAATGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_24847990_24848482_1:0:0_1:0:0_142/2 +CCCTTTATGTGACTCTATCACATATATCATTCTCATCATCAGCTTGGAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_25453923_25454484_1:0:0_2:0:0_143/2 +TTTTTATTTTGTTTTGTTCTTGATTGTTTGATTGTTTGTTTGTTTGAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_35396075_35396608_0:0:0_1:0:0_144/2 +AGGATGACAGTCATACTCAGACCACCATGGCACAAGCCTAGAGACCAGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_184356181_184356676_1:0:0_1:0:0_145/2 +CCTGGCTGGCCAGTGAGACCCAGGATCAATCCATCTCTGCCTTCCCCAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_87890172_87890679_0:0:0_1:0:0_146/2 +TGAGGTGCAAGCATCTGTGTATATGAGTAAAGACCAGAAAGGAGTCTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_192825121_192825655_0:0:0_3:2:0_147/2 +TTTGTTTCTTTCTTTTTTTCTTTCTTTCTTGCTTCCTTCCCTCCTTCCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_29477154_29477657_0:0:0_0:0:0_148/2 +AATGACAGCATCTTCAATAAATGGTGCTGGCACAACTGGCAGTTATCATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_68360607_68361138_2:1:0_2:0:0_149/2 +GGTCATGTCCTCTTTCTCCGTTGAAGAGGAGGGAATCCGTGTGGGGGAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_90679374_90679891_2:0:0_4:0:0_14a/2 +AGTGGGAACATCTGGACCCTTGGCTCCGTAGGCTTATCCCCTTGACAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_90921852_90922384_0:0:0_1:0:0_14b/2 +AGGTAGATCTTGGATCGGGAGTTGGGGAGAGTGAGGTGCACTAGCTGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_144744406_144744790_0:0:0_3:0:0_14c/2 +AGTCTGGCGGTTTCTCAGAAAACTGGACATAGTACTACCGGAGGATCCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_157579434_157579959_0:0:0_1:0:0_14d/2 +AGCCAAATGGATGGACCTGGAGGGCATCATCCTGAGTGAGGTAACACAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_22354013_22354577_0:0:0_2:0:0_14e/2 +TCTTGAGTTCAAGGCCAGACTGGTCCACAGAACTAGTTATAAGACAGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_14011029_14011557_0:0:0_1:0:0_14f/2 +CCACCACAAGACTTCGCTACTAAGTCCGAAAATGAGAATGTGCTATTAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130418472_130418955_2:0:0_2:0:0_150/2 +GGAGTCTGGTGACTCAATCTCTGGATTTCACACCTGCAATAAACCAGCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_150912771_150913298_1:0:0_0:0:0_151/2 +GAGACTATGCTGGGGCCTAGCAAACACAGAAGTGGATGCTCACCGTCAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_122600000_122600452_0:0:0_0:0:0_152/2 +AATTTCTAAAATATATAAAATTGTATAATATGATAGAAATGCATATTTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_172852130_172852552_1:0:0_2:0:0_153/2 +TAGCTGAGTAGTACTCCATTGTGTAGATGTACGACATTTTCTGTATCCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_58219252_58219809_1:0:0_1:0:0_154/2 +CTCTCTTTGCTTTCAAATTTATGGACTCCATTCTTGTTAATTACTGTTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_154116562_154116985_0:0:0_0:0:0_155/2 +TTTTTTTAGCTGCTAGGCTTTTGTCTCAGATCAGGATGGTGAGAAAGAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_169424620_169425179_1:0:0_0:0:0_156/2 +TGGCATGAAATGAATGAAAAAAGAAAAAAAGAGAGAGAGAGAAAGAGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72776580_72777093_1:0:0_0:0:0_157/2 +TGAGCAGGCCTAGATTCAGTAAATGGATGGATGACTAAATGGATGGGTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_102420738_102421205_2:0:0_1:0:0_158/2 +GGACATTTTCAAAATATCACAGAAGCAAGAAGGACCAAAAGCATAGATTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_148315363_148315906_2:0:0_0:0:0_159/2 +AAATGCCATCCTAACAAAAGAAATCTACAGATTCCATTCAATCCTCATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_93257911_93258453_0:0:0_1:0:0_15a/2 +CTCAGCTTTCCAATGATTGAAACAAGCTTAGACTCTGACATAGGCCCATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_94169994_94170446_0:0:0_1:0:0_15b/2 +AGGGCAGGAAGAGTGTTCTGTGTGTGGAACCTGGTGGCTGGAGGGCCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_126263407_126263894_2:0:0_2:0:0_15c/2 +TGTAATGACCGTTATGTGAGCAGCTGGGGAGAAAAGGCAGGTTGTTTGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_42763327_42763896_1:0:0_0:0:0_15d/2 +AGCCAGTATCCTTTACCTATAAATACCAAAATAAATAAATAAATAAATAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_127932894_127933379_0:0:0_2:0:0_15e/2 +TAAAATACTCACATGCAATGCTGGTGAGGATACCCATCCATCCTATCGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_83608654_83609158_1:0:0_3:0:0_15f/2 +TCCCCTACCCACCCACCACTCCTGTCTTCCCAGCCTGGCATTCTGCTACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_47669914_47670464_0:0:0_0:0:0_160/2 +TGGTGTTAGGCTCTTGTGCATCTTGAGAGAGTTTAAGAAATGGAGTACCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_133731323_133731869_1:0:0_2:0:0_161/2 +TTTTTTTTTTAACGATTTATTTATTGATTATATGTAAGTACACTGTAGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_133255321_133255920_0:0:0_1:0:0_162/2 +CTCACTGTCCTCTGTGCTTTAGGATTCTTGCAAGGCCTTTTGAAGTTCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_23328420_23328852_0:0:0_1:0:0_163/2 +ACTCAGGACCTCTGGAAGAGCAGTTGGTACTCTTAACAGCTGAGCCATCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_53072730_53073291_2:0:0_0:0:0_164/2 +CTGCACGCCCATGTTTATTACAGCATTATACCAAGAACAGCAAAGTAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_173130259_173130757_3:0:0_2:0:0_165/2 +CATGCTCTCACTAGTCCAGGCTCTGGCCATATACAGGCTGCCATTTTGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_87397192_87397710_2:0:0_1:0:0_166/2 +AATTTTCTGCTCAATCTAGCAAATAAGACATTTTATCAAGAAACTATATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_187438711_187439219_1:0:0_1:0:0_167/2 +GAAAAGGGGATGGGTGATGGAAAATGGGGAAGAGGCTGTGTGAGGGGGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_123461089_123461580_0:0:0_1:0:0_168/2 +CAAAATGAAATCTCTATCACAGAGACTTGATGCTACAATCCTCCCCAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_181088135_181088642_2:0:0_2:0:0_169/2 +AATCGGGCTTCCAGTTACAAAGTCAGCATGACTCCCTTTTTTGGGAGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_167764494_167764902_0:0:0_1:0:0_16a/2 +CCCACCTTCCCCATCTACCCGAGCTCACTATGAGGAGTGCCAGGTTTGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_157283727_157284210_1:0:0_0:0:0_16b/2 +ACTTCTTTCTAAATCATTGACAGAACCAGTTCCAAATGTACGATAGGTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_156428357_156428913_4:0:0_3:0:0_16c/2 +TATAGAAAACACTAAACCCCTAACTTTGTCGACAAATAATAAGTAACCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_27945156_27945679_0:0:0_2:0:0_16d/2 +TGGACTCATCTATACTCTCCATTTTCTATTTTTTAAATTATTTTAATTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_190959090_190959565_0:0:0_0:0:0_16e/2 +CACTTTCTCTTAGTGTCTCCACGGGCTCTGGAGGGACAGGGACAAGTGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_163184140_163184589_0:0:0_1:0:0_16f/2 +ACAGAACCGACACACAATTCAAACCAGGTTAATTGGTAAGATGTGGGGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_104189461_104189906_1:0:0_1:0:0_170/2 +CCTGCAAGATTGATTTCTGAAGGGTTGTGTTACTTTTCACATCCACTAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_77562742_77563170_2:0:0_0:0:0_171/2 +TACACGTCACTTTTTTAGACAGACATGGGAAATGAACTTCCTTTTTATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_192763088_192763581_0:0:0_0:0:0_172/2 +GGGAGCTGCTGAGATCTACGGTTAAAAACATTTTCTATTCATGAAATTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_36839841_36840369_1:0:0_1:0:0_173/2 +GGCAAAGTAGTAGTAAGTAGGGGCACTGTGATACTTGTTTTATCATAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_114603035_114603542_0:0:0_0:0:0_174/2 +ACGTTCATTTTCAATTAACTCTTGTTTACTCATCAAGGTTCTGGTAACCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_57790506_57791066_2:0:0_0:0:0_175/2 +GTTGGTAAAGAAGTTCTGTCAGGACCTGAAACTTTCCTGCTTACTGGGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_35650713_35651282_0:0:0_0:0:0_176/2 +AACTGAGAGATGTATTCATCTGGCTGCTTTCCGCTGAGTCGGGGCAAAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_9711969_9712380_0:0:0_3:0:0_177/2 +ACAGTTGATGCCCTCTTCTGGCCTCTGCAGGCACATATATGATGCACAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_89016556_89017046_1:0:0_0:0:0_178/2 +CTGGTGGTTCACTGTCAAGAAACTAGATGGATTGTGACACATGTGATCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_132197564_132198148_2:0:0_2:0:0_179/2 +AGTTTGAGAACCACTTGATTAGAAAATGGTGTAACTCCCTGCACCAATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_104335733_104336245_1:0:0_3:0:0_17a/2 +AATACCAAATAGAAAAATGTGAGGCATTATAAAGCCAATTAATGCACATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_75633066_75633602_2:0:0_1:0:0_17b/2 +GTACCTTTGGATGGTATAGTAATCAGGAGCTCTCCAAAGGACAAGAACTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_189869166_189869657_0:0:0_1:0:0_17c/2 +CTACCTGAGTTTGGTCCCCAGGACACGCACAAATAAATGTCATAAATTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_27940779_27941192_2:0:0_0:0:0_17d/2 +TGTCTATGTGCTCTGGTTAGGACTTCACATACTATATGGAATAGATAGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_116796056_116796571_1:0:0_1:0:0_17e/2 +ATATGTACTTCCTGAAGTGGTCCTCTGGCTTCTATTATTTTGCAAAACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_20487571_20488054_3:0:0_1:0:0_17f/2 +TGGGGTGCCCATGACTAGGTGGGGTGGGAGTGCTGCGTTCTGATGATGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_70106451_70106893_0:0:0_2:0:0_180/2 +CTTTCTTTTTTTCATTTATTAGATATTTTCTTTATATACATTTCAAATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_138350547_138351128_3:0:0_0:0:0_181/2 +GTTTAGTATCACGTGCACACACGGGCCCACCCATAAGTGTAATACATATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_103571822_103572343_2:0:0_1:0:0_182/2 +TTCTGCTAAACTACTATCTACAGAAACAATTAAGGAAATGGGCAACTATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_185391115_185391738_5:0:0_0:0:0_183/2 +TGGGTGTCCTGCGTAGCAAACAGGGTGTTGGTGCTTACCGCAGCTTTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_121389447_121389902_0:0:0_0:0:0_184/2 +GCTGCATGTGTGAGGATTTTTTTAAAAAAAGATTTATTTGTATTTGTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44088278_44088819_1:0:0_1:0:0_185/2 +TTTTATTTTTCTGAGAGTTTTCACACATGCACTCAGAATGCTCACACAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_57600248_57600747_0:0:0_3:0:0_186/2 +TTAATGGTTTCCTTTGTACAGCATCCATTAGTGCCATTGAGGCTGTTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_105765709_105766274_0:0:0_4:0:0_187/2 +CCATCACCTAGTCCGTATCACAGAGATACAGAGTGAAATACGTTGTCTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_158039847_158040318_0:0:0_1:0:0_188/2 +TCACATCTAGATTCAGCTGGCAGTCCAGGCTTCAGCTCCACTCACATTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_100649250_100649781_0:0:0_0:0:0_189/2 +TAGAATGGGGATCCTGGAGAGAAGGTTCAGTGGTTGCAAGCACCTTTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_92627120_92627576_1:0:0_1:0:0_18a/2 +TCTAACCCAACTGACTAAAATCCGTGCTGTCCGTACAGATGTGGGTAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_47045474_47045999_2:0:0_2:0:0_18b/2 +CACAACAAGATGCAGTTGTATTGTTATGGTGAGGCCAGCAGAGATGACTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_58859721_58860237_3:0:0_1:0:0_18c/2 +TCAGCAAATTGTACGTGCAGAGCGAGGTAACATCAGTTCTGAGGGGCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_38899259_38899748_1:0:0_2:0:0_18d/2 +AGCTGCAGAGAACTCACAAGGAATATGCCAATGTGGCCTTGGCTGGATCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_43169971_43170448_3:0:0_0:0:0_18e/2 +GAACTCAGGACTGATGGCAAACTAAGGAGCGATGGTAACTTTCTGTCACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_169159076_169159522_0:0:0_2:0:0_18f/2 +GTCTTTGTATGCAGTTAGGCCCCCAACTCATAGAGACCTGCCCCTAGTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_14622737_14623201_1:0:0_0:0:0_190/2 +TTGATCAGTAATTGAGAAACTGCCTTACAGTTGGATCTCATGGAGGCATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26821729_26822157_1:0:0_3:0:0_191/2 +GATTTTTTAGTAGGGTTTTATTTCAGTGAAGAGGCACGATGACAAGGGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_146737011_146737509_0:0:0_0:0:0_192/2 +AGGGAATCTTAGTCTGTGTTGTAGACTACAGACGTATCTGCACTCACACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_132937628_132938130_1:0:0_0:0:0_193/2 +CAGGAGCTGTATCTCAACCATAACCAGCTCTGCCGCATCTCCCCCAGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_108674541_108675003_0:0:0_0:0:0_194/2 +GTTTATATAAGGCCTGCCCTTTGCTGGAGCAAAAGAAGGAGGATGAATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_155314929_155315340_1:0:0_2:0:0_195/2 +AATAAAATGGCTGTAGGAATTCTGATAGGGATTTCATGAAATGTGTAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_76995369_76995845_0:0:0_0:0:0_196/2 +AGGGTTGTTTTGATTTGCATTTCTCTGATGATTAAGGATGCTGAGCATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_88758655_88759125_1:0:0_1:0:0_197/2 +GTTGTTGTCCTGGGCGGGTGATGATGTTTAATGCCGGGAGAGGAGGAGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_179447008_179447452_1:0:0_1:0:0_198/2 +TGGGATGCGTACCACAGGTCAGAGGACAACTTGTGGAGGCCAGTTCACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_70539778_70540384_1:0:0_0:0:0_199/2 +TACCAATTCTGAATTATGTAGCTTTTATGTATCTCATTATTATAAATAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_171297998_171298490_3:0:0_2:0:0_19a/2 +ATAACTTTGATCTGAACCAACCACCGGACAGCACTTCCAGCACGTTAGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_4703882_4704398_1:0:0_1:0:0_19b/2 +AAATGATGCTTTTGGGTTGTTTTGGACCCTCTCCATAATGTTTAAATGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_148373552_148374029_0:0:0_2:0:0_19c/2 +ACAGTAGGCTGTGAATATAATTGTTTTTCACCTTCAGGAAAAGGCTAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_165037832_165038374_1:0:0_2:0:0_19d/2 +CACAGGCTGGAGTTATCACAGAGACAGGAGCTTCAGTTGGGGAAATGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117911191_117911633_0:0:0_2:0:0_19e/2 +GCTTCTGGCTATTATAAATAGGGCTGCTATGGATATAGTGGAGCATTTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_101942751_101943298_2:0:0_2:0:0_19f/2 +GCGAAGGAAATAGATACTAGCCACATTGCCCTGGCGCCATGTAGACAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_159291114_159291545_1:0:0_0:0:0_1a0/2 +AACACCCCCACCCCCCCCACCCCCCCGCACGTTTATGGTGCTCGGTTGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26628880_26629394_1:0:0_1:0:0_1a1/2 +TAGGCGTTCCCTCATGCTCCTGGAACTCTGGGTCCTGTTGAAGTTACCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_18997387_18997869_1:0:0_1:0:0_1a2/2 +AAGCAAAATTGGAAAACTAGTTTGGGAATTCCAGAGTAGTATTGGTATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_39575593_39576071_1:0:0_2:0:0_1a3/2 +GGAAGCTAGGATCTCTCAGGAGCCTTGTGGAAAGATGGTGTGTGGACAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_5509844_5510306_2:0:0_1:0:0_1a4/2 +ACACAGCTGGAGTTATGTCAGAGAAAGGAGCTTCATTTGAGGAAATGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_109704460_109704956_1:0:0_0:0:0_1a5/2 +GTATTCAACAAATGAAAGAAATACACTAATAACATTATTTTTACTATGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_156587931_156588493_1:0:0_1:0:0_1a6/2 +CGCTGACTCCAGAAGCTACTGGCAGTGGCTGCTGGGAGAGAGAGTCACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_176610586_176611106_1:0:0_0:0:0_1a7/2 +CTTTTGCAATGTGATTAAAAGAAATGCCATCCATTTCCATGTTTTTAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_180872448_180872981_1:0:0_3:0:0_1a8/2 +GGCTTCACCAATAGCTTCTCACAGGCTCTCTTCATGGTGTGAAGCCTCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_26474215_26474717_2:0:0_1:0:0_1a9/2 +GTCCTCTGATCATTTCTGCACATGGAGCGGTTCTGAGATTGGCGGATGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_104541278_104541749_1:0:0_0:0:0_1aa/2 +GATTTTTATTTTATTTTATTTTATTTTTTGATTGGATATTTTCTTCATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_67015960_67016373_2:0:0_1:0:0_1ab/2 +ACACCCAGACCAACATTTTTGTCAATAAAATAAAACCCTGTCCTCTATTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_29940243_29940732_0:0:0_1:0:0_1ac/2 +GTTTCATTCCAGGGATGCAGGAATTGTTTAATATATGGAAATCCATCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_193079402_193079850_1:0:0_6:0:0_1ad/2 +TCCAGCTCAAAACATCATCAGAAACAGAGTCTACGACTGAAACTGCTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117439972_117440528_1:0:0_0:0:0_1ae/2 +AAAATCTGCCCAACTAGATTAGAGAAATTATCTCAATATTCTAACCTTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_177239334_177239795_2:0:0_1:0:0_1af/2 +GGGTACTGGTTAGTTCATAATGTTTTTCCACCTATAGGGTTGCAGATCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_158414545_158415096_3:0:0_0:0:0_1b0/2 +TATCTATCACGAGTGTATAATCTCAAGCCCTCGTCCTAATTTTGAAACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_97093485_97093964_1:0:0_0:0:0_1b1/2 +GGTCCAACTAAAGAAAGATGTCTCTGATATCACATTCCTGGTGCTTCAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_67614138_67614777_0:0:0_0:0:0_1b2/2 +TTATTGCTCATCCTGAATATGAGCACACACACACACACACATACACATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_153549562_153550076_0:0:0_1:0:0_1b3/2 +GGCAGGACTGGAGCAGTAGTGTCAGTCTAGAGCGCCAAGTGGCTGCTAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_55425424_55425904_0:1:0_0:0:0_1b4/2 +AAGAATCCAGACAGATGAAAGTTTTTTTTTCTTATTAAAGAATTACCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_191019412_191019908_2:0:0_1:0:0_1b5/2 +GTGTGCACACTGCTGAAAAAGGACGCGTTTCTCTTACTGTTTTCGTACCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_73180421_73180945_2:0:0_2:0:0_1b6/2 +CTTGAGTTCTTTCTATATATTGGATCTGTTCTTAAGAGCTGTCTCATTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_38129466_38129932_2:0:0_2:0:0_1b7/2 +CGGGCGGCAGCTTGGTGATGCGGCGGGTCCCGCGCCACCTCCGCCCAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_133540103_133540570_0:0:0_0:0:0_1b8/2 +CACACACACACACACACACACACACACACGCTTGTGCACATACGTGCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_184916633_184917139_2:0:0_2:0:0_1b9/2 +AAAGAGAAGATCTTGTGGATGGAAATCAAGGCTGCTCTGTCCAGGTAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_175669652_175670114_1:0:0_1:0:0_1ba/2 +CAGGGATCCCAAAAGTGTGGTTCCATTTTACAACACAGCTTTGAGTACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_8296849_8297319_1:0:0_0:0:0_1bb/2 +GAATTTGAATAACTACTCATTTACATAAGACATCACAACATTACAGTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_152905590_152906078_1:0:0_1:0:0_1bc/2 +AGTAAACATCAAAGACAAGTCATCAGTGAACAGGCCAACGAGCGGGAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_114902352_114902833_0:0:0_0:0:0_1bd/2 +CCATGGAAGGAGTTACAGAGATAAAGTTTGGAGCTGTGATGAAAGGATGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_192964279_192964734_0:0:0_0:0:0_1be/2 +TCTGAAGAGAATGTTCAAAGTTTCATTTCATTTTTATAACTTCTGACATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_38321189_38321768_1:0:0_3:0:0_1bf/2 +TGTCCAAACTGAGCTCAAAAGCCTCCTCTGTAGCTGCTTGAAGGAGATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_78900626_78901065_0:0:0_0:0:0_1c0/2 +TCAATTTACTTCTCTTTGACTGCCTTGTGCTTCCAAAGAAACCAGAAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_113540760_113541176_0:0:0_3:0:0_1c1/2 +GTACATACTAAAGTTGAATGTGTCAGGCAAATAAATTGAGAGACTATAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_130677359_130677835_0:0:0_1:0:0_1c2/2 +AACACTGCCTTTTCATTTCTAAGGAGTCTTTTCTTTCTTACTTTTTTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_180204210_180204758_2:0:0_0:0:0_1c3/2 +TATAGATATTTTAAGCCAACAACAAAGCTATTCTGGCGAGGGATCACATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_192984278_192984850_2:0:0_5:0:0_1c4/2 +ATATGGAGTGTGAAAAGATGTCAATGGACATAAAGCAAGTGATCTGAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_176155520_176156071_0:0:0_4:0:0_1c5/2 +GGCCGATTCTCTACTCTAACAGAATGACAGTGTGTCAGAAGGATCCAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_11299746_11300227_3:0:0_1:0:0_1c6/2 +TACTCATACAACAGATAAAGGCAGTGGAATCCTTAAGACAGGTTTTAACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_40475921_40476533_1:0:0_0:0:0_1c7/2 +GCTGGTTTTCTTTCCTTTTCAAAAGATGTTAGGTTTTAAGATTCTGTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_161162459_161162939_0:0:0_0:1:0_1c8/2 +TGTGCATGAGTGTCAACGTGTGTGTGTGTGTGTGTGTGTGTGTGTACCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_56968239_56968712_1:0:0_4:0:0_1c9/2 +TCAACTTGGTGATACAGTCCGACCACCCATTCCCCCATCCCTTATGTCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_90357627_90358090_2:0:0_1:0:0_1ca/2 +ACACATACCATCTACCAAAGACATGTATACACATACACCACACACCACAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_184900782_184901265_1:0:0_1:0:0_1cb/2 +GAGCGAGCACTGGCACCTGCGGCTCACCTGGCTGTGTCGGCTCTGCCGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_34520052_34520514_0:0:0_0:0:0_1cc/2 +AGAGAGGTGGGAGGGAAATAAGAAGAGAGTGGGGCAGGAGCAGGAGCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_121381246_121381739_0:0:0_0:0:0_1cd/2 +TGCTATCCAGATGTAAAGTGAATAAATAAATGAAAAAATTGAAAAAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_80355344_80355825_1:0:0_3:0:0_1ce/2 +GCTAACCAAATCCAAGAACACATCAAAAGAATTATCCATCCTGACCAAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_23025664_23026100_0:0:0_2:0:0_1cf/2 +GAGTATGGTGCCACTATGTCTTGCTACTATAAATTTCAACTCAAAGCAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_126877190_126877687_2:0:0_0:0:0_1d0/2 +AGAGTTCAAGCCTTTGTCCATTTCTCAACAGGAAACAGACAGGACCTTCA ++ +22222222222222222222222222222222222222222222222222 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++ +22222222222222222222222222222222222222222222222222 +@chr1_140999216_140999698_1:0:0_1:0:0_1d8/2 +TCCTCCATGGATGGGCTTGAGAAAGGACCCAAGACTAAACCACCAAAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_148512883_148513388_0:0:0_1:0:0_1d9/2 +CTCTCTTTCCACTGATGGCTGACTAGGACATCTTCTGATACATATGCACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_95472009_95472435_1:0:0_0:0:0_1da/2 +GGTTGCCTTTGTCCAGCTTTTATATGAGGGCTGTGTGCCTAGTCCTAATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_19217196_19217734_0:0:0_1:0:0_1db/2 +TGTGTGTGTGTTTGTGTGTGTGTGTGTACACGTGTGCACGCGCGTCTTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_4075909_4076300_0:0:0_1:0:0_1dc/2 +AAATTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTTCCTATTCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_186978576_186979074_1:0:0_0:0:0_1dd/2 +CAGAACAAACCAGAGCCCCGTTCATTGTTTTCTGTGGCTTTTGCTATGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_112188833_112189331_0:0:0_1:0:0_1de/2 +TTCAACCTACTACAACTCCCAAATGAATTCCAAAGCATTCCATTGCTTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_173609986_173610514_0:0:0_0:0:0_1df/2 +TGCTCAAGAAACAAAGGTGGGACAGTGAAAAAACAACTGGATAAAAGCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_22017871_22018438_0:0:0_2:0:0_1e0/2 +AGTTCTTAATTTAATAGACTCAGTACATCTTTAGAGTGCCTTGTTTTAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_48541209_48541729_1:0:0_2:0:0_1e1/2 +CGACCCATACAAAGATGTATGAATCTCACTTAGGAAGGTGAATAAAATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_10384181_10384617_2:0:0_0:0:0_1e2/2 +CGAGACATGATAATCAGAACAACAAATGGACTAAATAAAGATAGAATACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_20392227_20392827_2:0:0_0:0:0_1e3/2 +CCCTGACTAAGACACTCTGCTATGCTTGCAGACAGGCGCATGTTGTCCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_171278949_171279483_0:0:0_0:0:0_1e4/2 +TGTTGAGCAAAGAAGCCCCCCTCCTCCCCCCGAAGGCCTATTTTGCTATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_58815142_58815652_3:0:0_0:0:0_1e5/2 +GGGGACCCAGTGTGGGTTCCTCAATGGCACCTATCCTCTGAAAAACTAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_157206264_157206747_1:0:0_3:0:0_1e6/2 +AAAGATTAAATTGTATGTACATTATTCTCTTTCATTCTCTCTTAGATATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130727486_130727887_0:0:0_1:0:0_1e7/2 +TCCAGATAACCCAACAGAAAAGGGATTTATCCCAGTTATTGATGAAGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_56227774_56228368_1:0:0_2:0:0_1e8/2 +GGTCTTTCATTGGGCTTCTTCCACTAAAGGAAACATGAGAAGAGTGGACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_163976865_163977422_1:0:0_2:0:0_1e9/2 +GGAGTGTTTTTATTGACAGGTGTTAGTGCTTTTATAAAAAAAAACTATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_75768405_75768873_1:0:0_0:0:0_1ea/2 +TGTTGTGAAACCTGAAGATGGAGAGAGACAGAGATAGATAAAAGAGACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_99777250_99777759_1:0:0_0:0:0_1eb/2 +GTACTGTAGACCAAATTAATAAACAACACATACAAATAAATCCAAGAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_6944229_6944786_1:0:0_3:0:0_1ec/2 +ACCTGATCTACCATGGAGCTCCAAGTAGGAAGGACAGAACTGATTGGTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_6751099_6751639_3:0:0_0:0:0_1ed/2 +GAGACTGGGATGTAAAGTGAATAAGTAAACAGAGTATTTCTTGTTTATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_28492407_28492923_0:0:0_2:0:0_1ee/2 +CCGCATAGTGCCAGTAACAGATGCAAGCTTACAACTTGATCCCCACCTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_25977449_25977911_3:0:0_0:0:0_1ef/2 +TTTCCCCCCATTCAAGTCTTTTAGTTTGTTCTTGTGAGGCACTGAGTTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_180012197_180012695_1:0:0_3:0:0_1f0/2 +TGTGTGGAATACGATGACGATAGATGAGGCATTCTGTTTGATTTTCTGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_139551031_139551593_1:0:0_0:0:0_1f1/2 +ACTAATAGACAACCATTTACTCTGATTCAACTGGCTGCCAATTTCTGAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_88565594_88566005_0:0:0_1:0:0_1f2/2 +ACAGACAACATGGAGAACATGGGGAGGGGGCAATGAAAAGTATTAAAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_28334498_28334996_0:0:0_0:0:0_1f3/2 +GAGGACTCCAAAGGATGTCAAAGACTTCACAGTAAGTACTCTGGGCAGGA ++ +22222222222222222222222222222222222222222222222222 diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out5.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out5.fastq new file mode 100644 index 00000000000..6c482fa47c4 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out5.fastq @@ -0,0 +1,2000 @@ +@chr1_177668195_177668687_1:0:0_2:0:0_0/1 +CCCTTGCCTTCCTAGCTTTCAGTATTACCCACTAAGAACACATAAACATG ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_102240227_102240757_1:0:0_0:0:0_1/1 +AATGGATGCAGAAAATGTGGTACATCTACACAATGGAATCCTACTCAGCT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_135092709_135093083_1:0:0_0:0:0_2/1 +GATCTTGACATAAAGCAAAGGTTGTTAAACCAAGGCCTGCTTGCCCTGCA ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_173363751_173364238_0:0:0_1:0:0_3/1 +GAGGGCAGAGAGAAAATCTAAAGTGCAGTCTACTGGTCCTCAGTGGAGGG ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_155990043_155990565_1:0:0_0:0:0_4/1 +AAGCTTGCCGGTCTTCTGTGGGGCAGAGAACCCAGCTGCTCTTTTTCTAT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_3703883_3704401_0:0:0_1:0:0_5/1 +CTCTTGCAGGAATGAAGCCTTAACGAAAATAGACTGGTAGTGACAATATA ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_148211558_148212105_1:0:0_2:0:0_6/1 +AATTTCTTTAGTGATAATTAGTTTCTTGTATACTTTGCCCTCCTAACCAT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_30961675_30962138_2:0:0_0:0:0_7/1 +AAAAACAGGAAAACACATCCAAACAGGTAATGGAAATGAACAAAACCATA ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_86070681_86071151_1:0:0_0:0:0_8/1 +GAGCCACTTGCAGAACATTCTAATTGTTTCCAACTTTAAGAATAATTGTC ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_78259267_78259767_0:0:0_1:0:0_9/1 +TACCTTCACATCCCCCTCTACTTCTTTCCACCCCCGGTCACTGGGATTAT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_143451378_143451824_2:0:0_1:0:0_a/1 +TCTTTTTGTCTTATAGACGGTGTCTTTTGCCTTGCAGAAACTTTGGAGTT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_163539961_163540475_1:0:0_1:0:0_b/1 +GGCACACCTGTGATCCTGATCTTGAGGCTGGGAGATACAAGTTTCTGACC ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_70390520_70391012_0:0:0_1:0:0_c/1 +TCAGTTCAACATGTAGAAATCCCTTATGAATAATCTTGTCACTGTCATTT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_119090463_119090959_0:0:0_0:0:0_d/1 +GATGATGATGATGATGCCCAAGATGATGATGATATAGCATGCCTAAAACT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_12587911_12588392_1:0:0_2:0:0_e/1 +AGAAACGGCTAGCACATGATTAGTATCCTGTCCTCTCCCATGAGTCTGAC ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_21875665_21876102_0:0:0_1:0:0_f/1 +GCTAAAAGCAGTAAAGAATGAGAACACAGAGTGTTTAATGATATTACGGG ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_22900274_22900767_0:0:0_0:0:0_10/1 +TTCTTTTTTTTTCTTAGAAAATCAGTGTTTACTTATTACTTTTATTAATA ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_97511239_97511754_1:0:0_0:0:0_11/1 +AGAATTTTGGGTCCTGTTTGTGTAGCCAGTCTTTTAGTCTATGTCTTCTT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_64669865_64670428_2:0:0_2:0:0_12/1 +ACTCACATGATTGAGTTTCTAAAATCCTTACCAGTAATTCCCCCTGGAGC ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_69102786_69103213_3:0:0_1:0:0_13/1 +TTTTCAAAATAGCAAAAACTTTTTTTATTTTTTTGGTGTTCTGCTGCTGT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_117742994_117743506_1:0:0_4:0:0_14/1 +CCGGGATCAAGCTCAAGGAGATTGTCCTTGGACCTGACACTATTACTTAT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_53703453_53703930_0:0:0_1:0:0_15/1 +CGTCACAACATACTGAGCACCAGGAGCAAGTACTGCGGATCTGTGGGACT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_17968135_17968661_2:0:0_0:0:0_16/1 +ATCAATAGTACTGTGAAAGCAAATGCTGGTGAGGATGTGAACAAAGGGAA ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_126734590_126735074_2:0:0_1:0:0_17/1 +AAGGTCCCCCATACCCACCCCCCAATCCCCTAGCCACCCACTCCCCCTTT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_15473022_15473574_0:0:0_2:0:0_18/1 +GGGCTCTTCTCTTTGGTGTCATCCTCTGAAGTAGGAACCAGTTCATTAGC ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_32809503_32810008_3:0:0_4:0:0_19/1 +ACACGTGGTGTTCAGTGTCACCCCATGTAGATGGGGATGTTCCCTAGGAC ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_101160086_101160574_0:0:0_2:0:0_1a/1 +TGTGTGTACGACTGTTTCTGTGAAGGTAAACAAGAGGAGGTTGCACATGC ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_86845143_86845638_2:0:0_0:0:0_1b/1 +AGCCTTAATTAGTAGGGCTTGGTTTTTTTTGGGGGGGTGGGCTTGGGTTT ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 +@chr1_156394447_156394901_0:1:0_1:0:0_1c/1 +TAGGGAACTTTTGGGACAGCATTTGAACTGTAAATAAAGAAAATATCTAA ++ +17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 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+CCAAGAAGTGGGAGTGGGTGGGTAGAGGAGTGGGAGGGAGGGTATGCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_148211558_148212105_1:0:0_2:0:0_6/2 +TGCCACACTGTTAAAGACATTTATCTTCCCTCTTGAACACCAATCCCTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_30961675_30962138_2:0:0_0:0:0_7/2 +TTTCTGGTCCAGTCTATTTGGTTTTGTGTAGGCTTCTTGTATGATCATGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_86070681_86071151_1:0:0_0:0:0_8/2 +GTTTTATGATATCTTTACATATCCCATCTTTTAAAGTAGCCCTTCTATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_78259267_78259767_0:0:0_1:0:0_9/2 +AACAAAATCTGATGCACTTTTCTGGAGTATCTGAGGACAGCTACAGTGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_143451378_143451824_2:0:0_1:0:0_a/2 +TTGATAAAAACTTCATGGTACTGGTATAGAGACATACAAGTAGACCAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_163539961_163540475_1:0:0_1:0:0_b/2 +GAGGATGAATGAGTGACTTGAATTGGTGATTTTGAGGTCAAAATGTTTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_70390520_70391012_0:0:0_1:0:0_c/2 +AATTTTAAACATCTTATTAACTGAGATCAAAGATATTGATTTTCTATTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_119090463_119090959_0:0:0_0:0:0_d/2 +AAATGTTCACTTTGAAATCACTTCAGACCTACAGGAAAGTTACAAAGATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_12587911_12588392_1:0:0_2:0:0_e/2 +ATAATTTCACCTTTTGTCTCTGGGCGCTCATAAAAGATGCTATTGAAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_21875665_21876102_0:0:0_1:0:0_f/2 +GGGGCAGAAGACCATGCCACATGAAAGGACCACTTACAGAGCTAGTTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_22900274_22900767_0:0:0_0:0:0_10/2 +AATATATTTTAAAAATTCCCCATTGTGGTAGTGTAGACATAGGTCAGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_97511239_97511754_1:0:0_0:0:0_11/2 +TGCACTAAATAAAGATAGAATATTAAAAGCAGTAAGGGAAGAAAGGTCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_64669865_64670428_2:0:0_2:0:0_12/2 +CTTCTGGTTTTTCTGGCTTTCTACCCCGCAGAAAGTGATTTAGACTACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_69102786_69103213_3:0:0_1:0:0_13/2 +ATTTAAATTACACAAAATGAATATTCGAAAAAAGGTACCAAGTTAGTTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_117742994_117743506_1:0:0_4:0:0_14/2 +ACAGTCCAGTCTTCACTGACTGCTCCCCATCCCCTACCTCCTCCCCTCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_53703453_53703930_0:0:0_1:0:0_15/2 +TTCAACAGAAACCTTTCAGCACGGCTCATGCTTGGGTTGGTTATGTAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_17968135_17968661_2:0:0_0:0:0_16/2 +TAAATACAATACATGTTTGATTATGTGTGACTATTATCCATTAAATAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_126734590_126735074_2:0:0_1:0:0_17/2 +GGGCAAATGCTTAATTCTTTTGCTCTTCTCGTTTGAAGTTCTTATTGAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_15473022_15473574_0:0:0_2:0:0_18/2 +TCCTTCTAATTTCACGTTTTCTTTTTGTTTATAACACAGTGAGTTTCCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_32809503_32810008_3:0:0_4:0:0_19/2 +CAGGCAAGGCAACTGGAGCTGGAAGTTTAAACCTGCATGTTCATATTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_101160086_101160574_0:0:0_2:0:0_1a/2 +AGCATTGGAAATGTAAATGAAGAAAATACCTAATCAAAAAATTTAAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_86845143_86845638_2:0:0_0:0:0_1b/2 +GGCTTTCCTTGTGGCACTGTCCAATGTCCCTTTAAGGCAAAAGCATGAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_156394447_156394901_0:1:0_1:0:0_1c/2 +TTATGGCGAGATGAGCATCTCACTATAGAAATTAAAACTAATCAAAAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_175220096_175220545_0:0:0_1:0:0_1d/2 +TCTCATTCAATAGCCTAGACTATTACTTTAAATACAATAAAATTTAATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_66136304_66136892_1:0:0_0:0:0_1e/2 +AAATGGTTTTAGAAGTCCTTATCCTGGGCTTGGATCTTCTCATACCTCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_56699450_56700040_1:0:0_0:0:0_1f/2 +TCTTTTAAGTTGACAACTGAGTCTGAGCAGTGATGTTCAATGTATACTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_60449644_60450153_0:0:0_0:0:0_20/2 +GGGAACAGTAGCAGGAACAAGAGGGGTGGGGACAGATGCAGAAGTAGCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_28286517_28287074_0:0:0_0:0:0_21/2 +CAATTTTTCTCAGCTTCTGACCAAATTGCTCTGCTTGGCCTCATACTAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_127946423_127946897_1:0:0_1:0:0_22/2 +AATCCTCTTTGTGTAAGAACAGCTGGTGCTGTTAACTTGTCATCTCTCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_136274524_136275031_0:0:0_3:0:0_23/2 +GAGGGTGACTTGCTGAAGTCATTTCTCTCCTTTCACCATGTGGGTCCCCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_122372156_122372666_1:0:0_1:0:0_24/2 +GTTTCTGTGTGTCTGTATGTCTGTGAATGTGTGTGTGAGATTTTGTCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_19553027_19553520_1:0:0_0:0:0_25/2 +TTTGCGTATGGTGAAGTATGGGAGCCTTCTTACAACTGAAGAGGTGGTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_57071218_57071658_1:0:0_0:0:0_26/2 +CTGTGACTTGGTAAACTCCATGGGGTATCTCCGTACAAGGTGAATGACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_7557012_7557560_0:0:0_2:1:0_27/2 +CAGATTTCCTGACAGTCAAGCTGCCTCTGCATCCCTGAGATCATGCTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_18791508_18791966_0:0:0_0:0:0_28/2 +AAGCCAGAGTACGACTGCCCTTACATGAGCCCCATTCCCAATGAGCTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_56244256_56244708_0:0:0_0:0:0_29/2 +ATGTTTCCATTTGCATTTAGCTAAAAATTGGCAAGAAGATTGTCATCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_30613322_30613773_2:0:0_1:0:0_2a/2 +GATTGCTTCCAGCTTCTCTCCAATTACTTAGATGTTGGCTACTGGTTTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_161898116_161898586_1:0:0_1:0:0_2b/2 +CACTAATTGAGAAATGCCTTACAGCTGGATCTCATGTAGGCATTTGCCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_3742828_3743343_1:0:0_0:0:0_2c/2 +GTCTGGGAAGAACCCAACTGTGTTCTATTTAATCCTGCCCTCCTTCTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_59624032_59624611_1:0:0_0:0:0_2d/2 +ATTTATTTATTTATTTATTTATTTATTTATTACACTGTAGCTGTCCTCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_98734890_98735381_1:0:0_2:0:0_2e/2 +AGTAGACACAGTGATTGTACAACAGGACATCTGATGGGACATTAGGACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_170863521_170863976_0:0:0_1:0:0_2f/2 +GTTTTGATTGTAGCCTTCTTCTTCACTTGTAGATGACTGCTTTCTTGCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_111611961_111612483_3:0:0_0:0:0_30/2 +CCCACCTGGGACAGACTAAATGATGCTTAGTTAACTCTAAAATTTCTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_125730124_125730581_1:0:0_1:1:0_31/2 +ATCGTTCCCACATCTTGCTTTCTTATTCCTCACACCCACAACCACAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_10873266_10873801_1:0:0_1:0:0_32/2 +TTCACTGTAGTTGTAACAAATGAGTTGTTTGTTGTGTTTTATAAAAACAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_175631956_175632547_3:0:0_1:0:0_33/2 +GCCGAGGATGCTATTTAAACATACAAGGTGTCTCATATGAGACTGGGTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_20372115_20372592_0:0:0_2:0:0_34/2 +TGTCCTTCTTACCAGAATGGACAGATTGTGGAAACAGAAACATCTATGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_172022589_172023145_0:0:0_2:0:0_35/2 +GCCAGGAAAGAGGAGGAAAAAAATAGTCTGACAATACTGCCCCAGCCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_168140019_168140474_0:0:0_1:0:0_36/2 +AGGGATCTGCACAAGTTTGCAGGTGTCTAAGTAGGTCAGAGGTATCAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_12207936_12208461_1:0:0_0:0:0_37/2 +TCATCTCAGACTTGCTATTACAATATCTAATCTTATCTTCTGATAATTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_73438005_73438553_2:0:0_0:0:0_38/2 +TGGCGTGGAGGAAACACTGGTCTCCGTGGACGTCATTTGGCAGTTTTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_152770828_152771350_1:0:0_1:0:0_39/2 +CAGCTACAAGGAGGCACCCGGTCTCTAAAACAGCAAACCAACAAAGAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_23377131_23377643_1:0:0_1:0:0_3a/2 +ATTTTGTTTTTTTTTTAATCAACGGTAAATACACTGTGCATTATACCCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_101774130_101774651_1:0:0_0:0:0_3b/2 +GATCCAACAAAGATAGAGAACTTCAGACCAATTTCTCTTATGAATATCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_44505664_44506178_2:0:0_1:0:0_3c/2 +GCTGAGGGCCTGATTTTGCCTACTTTTGGACCCATAGGAACAATTTTGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_136585250_136585783_0:0:0_0:0:0_3d/2 +CTCAGATTGTCAGGTTTGTGGGACAAGTATTTTTTTTACCCACTGAGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_125479421_125479942_1:0:0_1:0:0_3e/2 +GACAGGATAGAGGCAGCTAGTAAGCCATGAGGGCAGAGCTTGGGGGCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_48288718_48289238_0:0:0_2:0:0_3f/2 +AAAAGATATAGACTAACAGACTGGCTAGACAAACAGGACGCAACATTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_162596088_162596584_0:0:0_1:0:0_40/2 +CAGGACAGCCACGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_114964476_114965085_0:0:0_0:0:0_41/2 +ACTCACCATTTTAGTGAGTATACAAGACAAAAACTTGAATAGTCTAATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_132214583_132215104_0:0:0_1:0:0_42/2 +ATGGTGCCAGGGATCCAAACTCATGTTCTTATGTTTGCACAACCTTCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_4422836_4423410_1:0:0_1:0:0_43/2 +TTTTATCACCACAAATATAAGTGGGCCAGTGAGAATGATCAATCCATTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72831428_72831958_1:0:0_0:0:0_44/2 +AACAACAAAAAAAAAAAACCTGGGCTAGCAAGATGGCTCAGTAGGTAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_17626572_17627059_2:0:0_0:0:0_45/2 +TTGAGGGAACACACATAGTAACCACCTACAGATAGGATAATTGGAAAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_122621502_122622050_0:0:0_1:0:0_46/2 +TAAACTAATTAATTATAATTTGAGGACAGGAGGGAATTACAGAACATACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_157981625_157982140_2:0:0_1:0:0_47/2 +GACGTCCTACATCCCTTCCAGGCTCAGCTGTTGGTTTTCCCTAGTTACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_86952334_86952916_0:0:0_1:0:0_48/2 +ATTTTGTCCTTCTCAATTTTTTTTCCTTTCTTTGGCTTTAACCTTGCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_56589802_56590323_0:0:0_5:0:0_49/2 +CATTACGTGACGGCATTACCCCACAGTACCCACTTTGCTATGCTATTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_44959275_44959852_2:0:0_0:0:0_4a/2 +GGGCACCTGTCCTCCGGTCCAGACGGTGGCTGGCTGTCCCCTGCCCACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_78655270_78655764_0:0:0_1:0:0_4b/2 +ATTATAGGTGCTTAGTGGGAAGCTTGATGACCTGAGTTCACCATGGGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_92742731_92743276_3:0:0_1:1:0_4c/2 +TGGGATGCTGAGGTGGGCGGGTATAAGGCAATGGAACTGGTCCATGGGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_133350357_133350894_2:0:0_0:0:0_4d/2 +GAGAGCGAGAGAAGGTAGAGAAGTAGAAGCCAGTCATTGCCATGCAGAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_18383798_18384307_2:0:0_0:0:0_4e/2 +AGGGGGAAAGCCTGTGCTTTTTATTAAAGCATACCTACTGGCTTAGTGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_94539200_94539737_1:0:0_1:0:0_4f/2 +AGTTTCAGCGAGAGACAGATAGATGAATGGAATAGAATTGAAGACCCAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_131360576_131361118_1:1:0_0:0:0_50/2 +CGTTCCTTCCTACCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_55802170_55802665_0:0:0_1:0:0_51/2 +GAAATACTGCTTTCTCGAGCCTATTAATTATCTTGATATGAACTGAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_160986523_160987031_0:0:0_1:0:0_52/2 +TTGCATTACAAGTGTGAGCCTCTGCATCTGCTTCGCCTACTGTGCGCAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_10207724_10208191_1:0:0_1:0:0_53/2 +CCTGTTAATGGCCACCAGATGGGAGAGGTTCTGAAGAGATTTCCTTCCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_186877031_186877586_1:0:0_0:0:0_54/2 +TCTTGCGCGCGCTCGACTGGGAAGGAAGAACGACGCTGCAACAGGATCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_76761957_76762468_0:0:0_4:0:0_55/2 +TGTTTATAATAGCGAGACGCTTGAAAGAACCCAGCTGCCCCTCAACAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_117599116_117599626_3:0:0_1:0:0_56/2 +TGGCAACAGCAACAGTGAGTGTCTGTGGTGGCTGCATCTGGGATGGACCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_174656805_174657230_0:0:0_2:0:0_57/2 +ACCACACTGTGATTCACAAAGCTAGGAAGCGCTCTCTTAAGTTCTCCCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_31215276_31215715_1:0:0_3:0:0_58/2 +AATGCCTTCCTGGGACTCTGACCAATGGAGCTAATTCCAAAGACCATACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_126165616_126166084_1:0:0_0:0:0_59/2 +AGGATGAAGATTATATGTGAAAGAAGCACTTTGGTAGAGGAAGACTGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_164029809_164030262_1:0:0_2:0:0_5a/2 +TGTTGGGGTGTGGATAAAGTGTATATGAGTTGAAAGGTTGATTTGGTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_121717872_121718374_3:0:0_3:0:0_5b/2 +TATTCTCATGCAATAAACACAAAGCAAATGAAGCCAAAGCTGATGCTCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_160410719_160411215_0:0:0_1:0:0_5c/2 +AGTGTGCTTTTTGTACAAAATCAACAAATGATTTTAATATGATAGTATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_100203985_100204499_0:0:0_1:0:0_5d/2 +GAAAGTCTTAGTTCCCATGTCTTACCAGCAGTCTAACTTGCCTTCTTGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_177503365_177503816_3:0:0_0:0:0_5e/2 +ACAAGAGGTATGTCTTGGTCTGCCTTACACTGTTTACTTAAGCTGCATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_164919242_164919704_1:0:0_1:0:0_5f/2 +CCCAAGCGGAGTAGACGGCAGGAAATAATCAAACTCAGGGGTGAAATCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_36958484_36958940_1:0:0_2:0:0_60/2 +ACCTTAGCCTCCTCCGAGCCGAAAGCCGCAAAGCAACTATTGTCTTTTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_99520185_99520697_2:0:0_2:0:0_61/2 +CGACCTGTGATGGTTTGTATATCCTTGGCCCAGGGAGTGGCACCATCTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_92584393_92584910_1:0:0_1:0:0_62/2 +AGCTACTGCTCTAACACTATATCTGTCTGCTTCCTGGCATGAAAATCGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_6665937_6666494_1:0:0_2:0:0_63/2 +TAATAATGATGTCAGCATTTCTTTCAGTGCCTCTAGGCCCTCTCTGACCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_103781308_103781731_2:0:0_0:0:0_64/2 +ATATGTATCAAAGACAACTCGTCCCAAAAGAACCTTTCTAGTCCTCTGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_35981688_35982179_0:0:0_1:0:0_65/2 +CCCTTCCTTGCTTCCTTCTGAAGAACCAGCTTGCCTCCATTTTAGGCTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_76873892_76874342_1:0:0_1:0:0_66/2 +TTCTGTAAGGCTGTGAATCACCCAATTTCTACATGTTTTCAGACCATGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_148924276_148924708_1:0:0_0:0:0_67/2 +ACAAACCGTAGATCAACTTTATTACCTCCTTTATTATATTTAGAGGTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_48352388_48352886_0:0:0_0:0:0_68/2 +AACATTTTACTATACCATTCAACCATCATTTGAGAAGTTTCCTCCTGCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_135109139_135109668_0:0:0_0:0:0_69/2 +CTGGCCAATGGAGATGCAGCCTATTGTCACAGACATGGTGACAGTGCACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_133271389_133271883_0:0:0_0:0:0_6a/2 +CTAACCAAGTTACCCCGAGAAGGGCTGTGCTCTGGAGCGGGGAACTTGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_143528403_143528953_0:0:0_3:0:0_6b/2 +AGTTTTATGAAACTCAGGTCAGCGATCCACACAGCACTTATCACAAGGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_60739061_60739616_3:0:0_1:0:0_6c/2 +TTAAGGAATAGTGATTTTTGTTTCCTGTTATTTTTGTTATTAGAGGTGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_86239673_86240187_2:0:0_0:0:0_6d/2 +ATGCGTGATTCTAAGGCTGGGCCGCTTGTCCTGAACTGTGTGTGCTGCGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_8425683_8426176_2:0:0_1:0:0_6e/2 +CTTGCTGTGTTTTCGTAGTCTTATACTTTGTGGGAACTAATCCACTGTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_34934564_34935093_3:0:0_0:0:0_6f/2 +ATTTATTCATGTATGCTTGAGTATTCATGTAGTAAAGAGAAGACAGCCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_43897170_43897709_4:0:0_1:0:0_70/2 +GATAAGGTCACAGTCTGTCAGTGATGCACAGGACAAATCCAAAACCCGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_64512455_64512956_0:0:0_0:0:0_71/2 +AAAGTCAGGAGAGGCTGAAAGCTAGGCCTCTTGTACCAAGCCACTAAGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72637152_72637620_2:0:0_2:0:0_72/2 +ATGCCAGTGCACTAACACAAAGCCTGGCATGGTAAGGGACATGCTCGTCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_149528405_149528902_2:0:0_0:0:0_73/2 +GTGAAATGATAGACACCAACCCGCTTAAAAAAACTTTCCACCCCAAATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_89951120_89951611_2:0:0_1:0:0_74/2 +CCTCGAGGTCGACTCCTCTAGCCCTGCATGGGATATGAGTCGTCCCCAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_108291981_108292457_1:0:0_1:0:0_75/2 +TTTTGGTTTGTTGAGGGATTACTTTCTTGATTGTTCTAGGGCGTGATTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130354891_130355474_0:1:0_0:0:0_76/2 +GATGTGCACAAACATAAAAAACACACACACATGCACACACAAAAAAAGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_166207187_166207634_1:0:0_3:1:0_77/2 +CTGAAGTCAGGCCTGGAACTCAAGCAGGACAGGATGCAGGCACAGATGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_178111549_178112035_3:0:0_3:0:0_78/2 +TGGACACAAAACATTGAGAATGAGATTGCAACAGGATTCTGTACTACAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_64705135_64705653_1:0:0_3:0:0_79/2 +AATGTACAGTGGGCTTGATATGAAAATATTACAACATATAATTAGATCGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_50237028_50237524_0:0:0_2:0:0_7a/2 +TGCAGCTTCTGGGTATTATAAATAAGCCTGCTATGAACATAGTGGAGAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_134752385_134752911_2:0:0_0:0:0_7b/2 +CATTCTCTCCTTTGTCTGGCAGTGCCACAGCACAGGGTGCCGTGAGAGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_168207741_168208312_2:0:0_0:0:0_7c/2 +GAATGACCCGAGATGTGAGGACTAGGCAGGTTGCTGGGAGGAGGCCATGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_151034392_151034882_0:0:0_0:0:0_7d/2 +ATTAAAGACTTTACAAAAACTAACCTCATGAAACTGAAAAGCTTCTGTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_149618965_149619431_0:0:0_1:0:0_7e/2 +TTAGGTCCCAACACTCACTAAAAAGACAAGGTTTTCCCGCCGTTCTCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_72479618_72480144_1:1:0_0:0:0_7f/2 +GGTGCCAACCACTGTCAAGCTAATAGCAGACTAAAAGTTTTACCGGAGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_18771436_18771929_1:0:0_2:0:0_80/2 +TAGTTTTCCAGTGAGGGCTAATAGAACAAAGTGGTATAAATGGTTCAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_177626454_177626877_2:0:0_1:0:0_81/2 +GGTGGTGCAAAGAGAGTCCTGAAGCTGCAGATAGAGTGACAAGAGAAGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_58671914_58672334_4:0:0_0:0:0_82/2 +ATTCTTGTGTGACCACGCCCCTAGGATCCTGGGATCCTGGGTGTGTTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_123634655_123635138_1:0:0_1:0:0_83/2 +TCATCCAGAGGTCTGGAATCTTGTTCACAGCACCCATATCTAGCAGCCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_32777949_32778514_0:0:0_2:0:0_84/2 +ATTTCCAAAAATTAAACTTGATCTTCATATTAACTTTCTAATCTACAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_38321026_38321532_2:0:0_2:0:0_85/2 +TTGCTTACATTCATGGTAGGCCTAACACCACCCAGCATCCTTTGCTTCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_31837668_31838221_1:0:0_2:0:0_86/2 +CCTGGTGTCATTAGCAGAGCCTGGTGGTTTCTGGATTTAACTGGCATTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_189752778_189753180_2:0:0_0:0:0_87/2 +AAGAGAGAGAGAGAGAGATAGCGAGAGAGAGAGAGAGAAAGACAGACAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_43602264_43602720_2:0:0_0:0:0_88/2 +TTGTCTTGAGCTGATGATGACATGAGACATTATCCATCTCCAAAATGCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_29558267_29558774_2:0:0_0:0:0_89/2 +AATTAGAAAGGGCAATCTGCAAATTCATGTGGAATAACAAAAAACCTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_59048796_59049203_1:0:0_0:0:0_8a/2 +TCTGGAACTATAGGACTAAACTTGATTGGCTGATGCTAGGGAGCAGCTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_31285666_31286194_0:0:0_1:0:0_8b/2 +AAACAAAACAAAACAAAACAGATTCAATCATGTTAAGAGGGATAACCTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_159055630_159056144_1:0:0_3:0:0_8c/2 +GCTCTCTCTAGGAAGGCTCCTTGTTGCCAGACGTCATCCTCTCATTCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_163934531_163935036_0:0:0_1:0:0_8d/2 +CAAAGGCTTACCTAAAACAAGCAGTATATGACAGCTAGCTGAAATAAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_116610918_116611481_1:0:0_0:0:0_8e/2 +ACTTAGAATTCTAAATAAAAGGTTAACTGTTTTCTTGGAATGCACTTAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_141208156_141208756_0:0:0_0:0:0_8f/2 +CTGAGTTATGCAGCCTTGCAGAAAGTTCTGGACAGGGTTACTTTTCAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_45492268_45492792_1:0:0_3:0:0_90/2 +AGTACATTAGCAGCCTCTGGAGAAAGAAGATATGCTGCAGTTTGGAAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_11755179_11755683_0:0:0_1:0:0_91/2 +GGGCTCCCACAAATATTCTAGTATGCTTTGCTCTAGGATAAATAGAATCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_156738022_156738530_2:0:0_2:0:0_92/2 +GATGCAGTATAAATGGTGTAGCAGATGCCCGAGACCTCAAACACACCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_95480426_95480839_0:0:0_0:0:0_93/2 +TTAAGTGATGTAACTGGATAACAGTAATGAAATTTTAGGTTCTCAGTGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_173460574_173461156_3:0:0_1:0:0_94/2 +TAAATACCAAAAAATGGATTTTGTCAAATAAGGTCTTATAATACCACATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_17445381_17445808_2:0:0_4:0:0_95/2 +TAGAAACTGGCAGCCTTTAATTGTCTTGTAGCTTTACCTCTTTGTATGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_76540003_76540477_2:0:0_2:0:0_96/2 +GTGTAGCTCATATGTGACAGCAAACATTGTCCTTGCTGTAACTTTTAGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_12896019_12896500_1:0:0_1:0:0_97/2 +ATCCCAGGAGCTTGGTCACACCAGGTTCTCAGGATCACAGAGGCAGCTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_41708628_41709145_0:0:0_1:0:0_98/2 +TACATGTGTGTATATGTGTGCATGGTGTGTACGGTGTGTATGTATGTGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_106826115_106826660_0:0:0_1:0:0_99/2 +TGTCTCATTTATGGGTCTTTAATTCTATTTTATTGATTGACATGTCTGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_13247654_13248181_1:0:0_0:0:0_9a/2 +ATCTGCAGACAGTTCTAACATCTGATGTTCATTTACTACAGACCAGTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117777350_117777861_0:0:0_1:0:0_9b/2 +AAATGTACTCACTGATAAGTGGATATTAACCCAGAAACTTAGTATAGCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_77191506_77192008_2:0:0_1:0:0_9c/2 +TAAAAAAAAAAACTCTTTAGTTTGGCTTGCATGTGATTCAAGGTTTCCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_36849743_36850269_1:0:0_1:0:0_9d/2 +TCTTTCTAGAACAGACTCCAGTTCAATAACCATTTATTGGTTGGGTGATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_148890840_148891366_0:0:0_0:0:0_9e/2 +AATCTAAAATTTGAACCCCTTATACCCTTCAAATCCACCATCAACTGTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_84671373_84671880_2:0:0_1:0:0_9f/2 +TTCTAGGGACATTCTTTTCTTTCTACAGATTTCGATAATTAAAGGAGAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_102434771_102435253_0:0:0_1:0:0_a0/2 +ACTTCCTCTTGGTTAGTTGTCCAGTGAGTTCTACATTGGTCTGTCTCTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_100209819_100210321_0:0:0_1:0:0_a1/2 +TCTAAATGGGATGTGGCTAAGCTGGCAGTTTGCTGGCTTAGCATTTATGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_62044005_62044573_2:0:0_1:0:0_a2/2 +GTCAGACATCAGCATCACAAATGCAGAATGACAGAAATTGACTTGCACCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_85132332_85132871_1:0:0_3:0:0_a3/2 +CAAAAGAAAACATTTAATTGGGGCTTTTTTACAGTTTCAAAAAATAGGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_58843215_58843696_0:0:0_0:0:0_a4/2 +CGTGCCAGAAGAAGAGAGTGACTCCTCTGGAACTGGAGATACAGGCAGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_137975188_137975732_1:0:0_1:1:0_a5/2 +TGGCCAGATACAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_141967561_141968074_0:0:0_0:0:0_a6/2 +TCAACATATATGACATCCATAAATCAATGATTTGACTATGAAACCATGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_8624607_8625140_1:0:0_1:0:0_a7/2 +TTAACTTTCAAGACAAGTGAATACTATATGATTTGGTGATTCTATGCAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_138783244_138783650_1:0:0_1:0:0_a8/2 +GATACTCATGTGTGTGCCCAGCGGCTCTTTGAAGCTTACGTTCTTACATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_52699200_52699639_1:0:0_1:0:0_a9/2 +TCGCCACCGTCTGCTGTCACCTGAATTTTTGATCTTAGCCCTTCTGACTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_32849205_32849709_0:0:0_0:0:0_aa/2 +AAGTCAGAGGAAGCAGCCAGAATTAGCTGGAGCACCATGAGAAGCACCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_182043596_182044137_0:0:0_0:0:0_ab/2 +AAAGAAAAGAAAAGAAAAGAAAAGAAAAAATGGACAAGAAGGCAAATAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_136004325_136004842_4:0:0_0:0:0_ac/2 +AATCAGCTAGTTGGTTTGTCAGAGGAACTCTCAAGAGAAGATAGCACTAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_174545541_174546018_2:0:0_1:0:0_ad/2 +TGTCTGAGGCATTCTGCAGAGCTGCGTTACTTTGTTTTGTTGAAAGGTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_11117502_11117925_0:0:0_1:0:0_ae/2 +CACTGCATATACTATTGACCTAGTCTGACATAATACCTCACTTTCCTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_44177515_44177974_0:0:0_3:0:0_af/2 +CTCAAGAAGAACTAAACCCACACAGAAGTACCTTGGTCAATATTTCACAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72645507_72646002_0:0:0_0:0:0_b0/2 +AGCCCCAATGAAATATTTCATGATGTTTCTTTACAGGAATAGAAACCCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_147283777_147284272_0:0:0_1:0:0_b1/2 +TGCTCCCTTTTATTTTTGTTGTTAGAGTTGGGATTCTGTTCTTGTGGCTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_133675964_133676447_1:0:0_0:0:0_b2/2 +CATGTCAATGTGTGGGTCTGTTTGTAGGTATGTGCCTGAGCGAGCAAGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_114568587_114569130_0:0:0_0:0:0_b3/2 +TCCGAGTTGGGGTTTACTATTCTTATTTGTTTAGTAAGATATTAAAGGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_111695385_111695895_0:0:0_0:0:0_b4/2 +TGATTTTCTCATCCGTAGATGAGTGGGCTTTTAACCTTGGCTTGGGTGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_172273320_172273788_1:0:0_0:0:0_b5/2 +AAGAAAACACTATTCCATAGGAACCTGAAGCCAGCTTCCCGTCTCAAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_29014340_29014871_0:0:0_2:0:0_b6/2 +GCAAGGCTCCATCTCCTACTAGCACCACTCCCTATGGGCCAAGTATTCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_177626521_177627066_1:1:0_0:0:0_b7/2 +GACCGGCACCTCTCACTGTGACCATTTTGAGTTTCTTGCTCTAAACTGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_110742845_110743354_1:0:0_0:0:0_b8/2 +CATCCAATAGATGACTGAGCATCCACTTCTGTATTTGCCAGGTACTGGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_14101155_14101687_3:0:0_0:0:0_b9/2 +CTAAGGTAAATTAGATCTTCCACCTTTGATTTACCCAGTTCTCCCAAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_38147934_38148475_0:0:0_0:0:0_ba/2 +TCCATCTGGAGTATTCAGAGGGCCCTTGAGGTTTGATGCTCATCCACGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_84834550_84834957_2:0:0_1:0:0_bb/2 +AGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGCTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_94046734_94047311_0:2:0_1:0:0_bc/2 +CTGTGGAACAGGAAGTCGAAAATTCTAATCAGGATTCTCTTGGTTAAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_138724568_138725155_1:0:0_2:0:0_bd/2 +GATCTTCCCTTGGCTCAGCATTATTAAGGAAGGTGCTGGCTGAACCAGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_105672406_105672966_0:0:0_1:0:0_be/2 +TCAATTACTACCATTTTGTGCATATTTTAAAAGCACACTATGGACACACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_157814995_157815529_0:0:0_3:0:0_bf/2 +TGACATACAAGTAATAAAGCCAAATACTTAAATAGGCCATCTCTGTTACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130059190_130059641_1:0:0_0:0:0_c0/2 +GTTGGGGGTTGGGGAAATCTTTAGGAAGTTCCAGAGACCTGAGACAGGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_18604367_18604942_1:0:0_0:0:0_c1/2 +TAGCGGTACACTGTGTGAGCTCTAGGAAAATACAGAGCTCAGGAGATTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_160029930_160030407_0:0:0_1:0:0_c2/2 +CAGATAGCTAGCTTATGGACTAAGATTTTTTTTTAGAGTGGCTTAGTACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_32417120_32417575_0:0:0_3:0:0_c3/2 +AGTTATACATGTTGTGGTGGACCCCAGCAACAAAATTACTTCCATTCCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_91572336_91572825_0:0:0_3:0:0_c4/2 +CACCTTCAGGAACTGTTAGAGGTGGTTCCTGTTGCTCTTACGCCCCCCGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_167308006_167308522_0:0:0_0:0:0_c5/2 +GCCCGATCGCCTACCTCACACTAGAACCCTGTCACACGGTGGCTGGACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_53658226_53658697_1:0:0_1:0:0_c6/2 +GTTCTTTTGTAATTGCGTTACCTCACTCAGGATAATGCCCTCCATGTCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_75542501_75543075_2:0:0_0:0:0_c7/2 +AAGTTCTCTCTCGCCAAGGTAGAAGCTAGAAAAATGCATATGTCCTGACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_49392954_49393517_0:0:0_2:0:0_c8/2 +GTATCTTTTTCTCTCCTTTTCATTTTTTAAAGTTTATTGTTGTTCTTAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_18890524_18891056_1:0:0_0:0:0_c9/2 +AGTTGATTCCGGACTCTTCAGAGTCCAGCTTTTTGGGGGTTTTGTTTTTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_13661516_13661931_1:0:0_1:0:0_ca/2 +AAAAGGAGTAGGCTAAGGTAGTGAATACACTCTACATCTCTATTGTGGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_69507936_69508419_2:0:0_1:0:0_cb/2 +CACCTCGAGAAAGAGCCAACCATAGAGCATGTGTGTTGATTGTTTAACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_171186227_171186672_2:0:0_1:0:0_cc/2 +CCCTTCTCTCTTCTAGAAACCAGACAATCCGTCCTTATACTCTCTAGTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_151167139_151167658_0:0:0_3:0:0_cd/2 +TCCAAATTAGACAGACTTCCTCTTCCTGTGGCCTGGACTGTTTTTTCTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_166490443_166490901_1:0:0_2:0:0_ce/2 +GATGTCAGAAACATGATAGGTCTCAGAATGTGAGGATTTTAATCCCAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_78053476_78053981_1:0:0_0:0:0_cf/2 +ATAGCATATCCCCTTAGCCAGAGAGCTTAGACTGGAGAAGCACAGCTGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_27573317_27573793_0:0:0_2:0:0_d0/2 +TTTAAGCTTATATAATAAAAAACATAATTACAAATCTATACAAAAGTATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_74520986_74521432_1:0:0_4:0:0_d1/2 +TTTCCTTATAAAGTCTGAGAGTTTAGTTAGTGCTGACTTGTCAGAAACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_194568812_194569255_1:0:0_0:0:0_d2/2 +AAGTACCATCTGTATTAATGATTCACAGTTATTTAAATATTTGAACAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_173094678_173095086_1:0:0_0:0:0_d3/2 +TAAGGTTGAGTTTCTGATAGGATACCATGAGGTAAAGATTTCCAAGCAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_125473775_125474200_1:0:0_0:0:0_d4/2 +GCAGCTTGACTCCGGTTGTGATTAATCAAAAGAGGTGACCCTGGGAGACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_60312834_60313394_2:0:0_1:0:0_d5/2 +GAAGGAACGGGAAGGAGAAATGGTGTAATTAAATTATAATCTCAAAAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_21769340_21769783_1:0:0_1:0:0_d6/2 +GGCTAAGATCAAAACTTCAGGTGACCGCAGATGCTGGCGAGGATGTGGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_29011734_29012196_0:0:0_0:0:0_d7/2 +AATCAGATTTTGTGTTTTGTTTGGTTTTCCATTAATGCTTTCACAACGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_55988735_55989188_1:0:0_0:0:0_d8/2 +AAGATTAGTTCTAAAGACATTACAGCTGCCACTCCAAGTTCTTGCCCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_143689772_143690244_0:0:0_2:0:0_d9/2 +TCTAGTTAATTAACACTGTTATTACTTTACATGTTGCTCCATTTTGTGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_102292799_102293241_0:0:0_2:0:0_da/2 +GAATACGATTACTAATTCGTTGAGAAGGTGATATGGCCATTCACAAAACG ++ +22222222222222222222222222222222222222222222222222 +@chr1_175815890_175816392_0:0:0_1:0:0_db/2 +AACATTTCAACCTCTCCATGGCACTGAAGTTTTAATCAGCCAATCAGGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_65030887_65031423_1:0:0_0:0:0_dc/2 +TAATGTTATTCCTGAGATTTTTCCAGAGAAACAAATCCCACCATTTTTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_77446136_77446727_1:0:0_0:0:0_dd/2 +GGACTACTTTCACTAAAGTGGAAAAACTCAATGGTGCTGTGAAACCTCGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_79825884_79826306_1:0:0_0:0:0_de/2 +CAGGGGAACACCAGGGCCAAAAAGGGGGAGTGGGTGGGCAGGGGAGTGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_142137580_142138145_0:0:0_1:0:0_df/2 +GCCTCTAACAGTACCAAGGCTAAGCTGTTCACTATGACTTCATACCTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_77524851_77525306_1:0:0_2:0:0_e0/2 +GCAAGCTCCCGAAATCACAAGTTTGCAGACCAGGCAATGGGAAATTAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26694201_26694676_0:0:0_0:0:0_e1/2 +ACAATCGAATCATTATCTAGATATTTTGATTATCTTTGCTTTAGGTTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_93157579_93158060_0:0:0_1:0:0_e2/2 +CCTTTGGGATTCTCCATCCAATGAGCCTCAGTTTCCTTACGAGAGGGGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_93554302_93554745_0:0:0_1:0:0_e3/2 +ACAGGATGCAGCTGGAGACTTCAACACCTTACCTCCAATAATAGTCATAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_115859373_115859816_1:0:0_1:0:0_e4/2 +GCATGCATCAAAGCAATGGTCCCTTAAAGCAGAGGAGTCAAGACTTTTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_59908209_59908731_3:0:0_0:0:0_e5/2 +CTTGTTGTCTAAAAGGACTGAAAGGCAAGATTGGCTGCTGAGGTACTTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_154628329_154628794_2:0:0_1:0:0_e6/2 +TGTACAGACACTTTATAGGTGTCTTTGGTGACTTTGGTGACACTCTGGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_38934187_38934653_1:0:0_1:0:1_e7/2 +TTATAGCTTGCAATAGAAAATGGAGTTTTGTTTTTGCCAAATAAATGGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_176440703_176441215_3:0:0_1:0:0_e8/2 +GGACCGAGCCAGTCTAGATATTGCAGAACTAAGAGTGTGTCTGTGAGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_146248574_146249007_1:0:0_0:0:0_e9/2 +GAATAGATTGTACAGAATCAATAACCTACCAAGCATTTGCCTAGGGACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_137417062_137417534_1:0:0_0:0:0_ea/2 +ATGCCCAGTCACCCACAGTTGGTCTCCTGTCTCAGCCCCAATAACTAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_55607180_55607772_1:0:0_0:0:0_eb/2 +GGCACATCATTATCCATTGGTAAGCTTTGCTTTTTCCACAAGGTCACTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_174928179_174928755_0:0:0_1:0:0_ec/2 +AATTGCAAATAATTTTTATCCCATTTTGTATGTATGATAACTGATACCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_113923154_113923648_3:0:0_1:0:0_ed/2 +TAATGTGAGGTTACCTCTGGCACTGAGGACTATTAAGTGGCTTTAAATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_78423064_78423594_1:0:0_0:0:0_ee/2 +AACTTGATATATGTTACTGTGGACCAAATGCCCTTCCTTCTCCAGTATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_154582561_154583019_0:0:0_1:0:0_ef/2 +CAGCAGCCTTGTTTGTAGTCTTATTATGAATTCAACAATATGTCACATCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_181723357_181723842_1:0:0_2:0:0_f0/2 +CATGGCCATTTTCAAGACTCAGGTTGTGGACATCACACTAAGTGAGATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_176206787_176207249_1:0:0_1:0:0_f1/2 +TGTGACAGTCTCTGGTGGCCTTACACTCCTCCTCTTTTTGCCTCTATGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_156026308_156026788_0:1:0_2:0:0_f2/2 +ATTTTATTTTCAAAGCACTAAATTATTAGAATATTTTACCTTTTTATATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_55128175_55128671_1:0:0_0:0:0_f3/2 +CAGAGCAGTGAGCGAGTTTCCTGGAGAGGCCCGTGAGGGGACAGTCACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_184447109_184447646_1:0:0_1:1:0_f4/2 +GTTATATAACCTCATAGCAGTCACCAAATGAAATAAGACATTCCTCGTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_194617734_194618226_0:0:0_0:0:0_f5/2 +GTGATTCTCACATTTATTCTTCCTCTATTATTGTTTATGTCTGCATGTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_80810218_80810755_0:0:0_0:0:0_f6/2 +AGAGAAAGGCAGAGAAATAGAAGAGAGAGAGAGACCTACCTCTGATAACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_144296368_144296930_2:0:0_2:0:0_f7/2 +ATAGTTCCTTTTGACATAGATCCTTCTAAAGGAATTGTAAGGGAATGTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_108312503_108312946_1:0:0_2:0:0_f8/2 +GTTAAACAAGCATGCAATCCCACCAACAATGTAGGAGTGTTCCCCTTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_78228179_78228640_0:1:0_0:0:0_f9/2 +CTGAGTCTTGTTTGAGGATGGATGAACTGATATAAACGTTTTCAAAAAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_52088998_52089426_1:0:0_1:0:0_fa/2 +CTGTCCTGTCTTCCCTCTCCTCCGATCCCTCTTCTGAGTACTGAGCTTAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_30782403_30782942_1:0:0_0:0:0_fb/2 +AATATATTCACCTACACCTGTTAACTCAAAGGATCTGCTTCAATACTTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_6435675_6436268_3:0:0_2:0:0_fc/2 +GACTCATTCATTCCCAGAGAGGAACAAAGGAAAATACCACAGGCATTTCG ++ +22222222222222222222222222222222222222222222222222 +@chr1_164237997_164238538_0:0:0_0:0:0_fd/2 +CATCAGACAGACTTCCAGATAAAACGGGTTTCAGATGAGATCAGTACTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_187097969_187098475_2:0:0_2:0:0_fe/2 +CCATAGCAGCTGTGTGGAAGTCATGACTCCTGGAGGTCAAGTGACTATAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44694856_44695375_3:0:0_1:1:0_ff/2 +TTCCATAATATCTCTTACTATCAATGGACTCAATTCGCCAATAAAAAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_111782668_111783223_1:0:0_3:0:0_100/2 +GCTCTATCCCGTGGATGGCTGTGAGCATCCCCTTCTATTTGTCAGGCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_94206847_94207360_1:0:0_1:0:0_101/2 +AAGCAAAACTGAGAAGCGGCAAGGAGGAGAGAACAGAATGGAACATCACG ++ +22222222222222222222222222222222222222222222222222 +@chr1_132119789_132120286_3:0:0_1:0:0_102/2 +GGCAGGTAGGCGGCGGGCGGACAGGCCGGGCAGCTCAGTGAACTCATATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_34226734_34227203_0:0:0_0:0:0_103/2 +AGCGGGCTACTGATAGCCCACAGGTTCAAACCAGACAAAATCACAGTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_138105716_138106319_4:0:0_1:0:0_104/2 +ATAAACAATCATGGCTCCTTAATTAACACAAATACTTTGAGGTCTCAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_126030856_126031342_1:0:0_2:0:0_105/2 +CAATTGTTGTAGAAACATTTCAAGAAAAGCGTGTATACAATTCACTAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_118807485_118808058_0:0:0_1:0:0_106/2 +TTCCGAAAAAGAAATAAGCAGAAAGCTGTTTGACTTTTCCTGGGGTGACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_19849114_19849606_2:0:0_0:0:0_107/2 +TTCCTTAGGGTGCTGTGGTGAAGGTCTTTTATGACAGCAAATGGCAAATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_66877733_66878136_2:0:0_1:0:0_108/2 +GAGCATCATAATGGCCCATCGGTATCAAAGCTAAGACACGAGCATGGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_132522495_132522987_0:0:0_1:0:0_109/2 +GCCCTGACTAGTGTAATAGGCCACAAGACGAAATGGAGCCTAGATTCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117050436_117050942_0:0:0_1:0:0_10a/2 +ACCCAATCACAAAAGAATACACATGATGCGCCCTCACTGATAATCGGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_125967212_125967705_0:0:0_0:0:0_10b/2 +TCAGGGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_69313718_69314189_1:0:0_2:0:0_10c/2 +TTTTCGTAGATGACACTATCACCTCTGCGTATCTGACCTCATCCTCAGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_60897368_60897871_1:0:0_1:0:0_10d/2 +TTCTCTAGCTTCTCCATTGGGGGCCCTGTGTTCCATCCTATAGATGGCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_174325015_174325549_0:1:0_2:0:0_10e/2 +TTAGAAATAACTTCAGAATGTCTTTTTGCCCCGTACAAATAAATAAGCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_85055965_85056468_2:0:0_0:0:0_10f/2 +CATAGAGAACATCGGCACAACAATCAAAGAAAATGGAAAATGCAAAAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_131415777_131416249_5:0:0_1:0:0_110/2 +TTTTGATCTCCTAACCAAAGGAAGATCTCCCAGTTTCATTGGTTCCAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_67136277_67136702_3:0:0_0:0:0_111/2 +GTGCCATTCTGCTTTACTCAAGTGTTCTCCGTTTTACAATTCAGGAAAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_8402131_8402528_1:0:0_2:0:0_112/2 +TAGTTCTTATTACCATTTGGTTGATTTCACCCCTGATTTTGATTATTTCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_155126875_155127345_1:0:0_3:0:0_113/2 +TTGGCCAGCGTGAGATACATGCGACCCTGTTTAAAAAAAAAAAATCAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_93916438_93916928_0:0:0_0:0:0_114/2 +GGCAGTGATGTCTGAGGAGGACTCTTTGGGCAGATCTGAGGCCTGCTCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_135734641_135735118_0:0:0_0:0:0_115/2 +GTTGGGCAACCAGTTCATAGCACCACAGCTGTAGGAGGCAGAACTGGATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44391025_44391499_0:0:0_1:0:0_116/2 +TTAGCCAAATTAGAGGGTCGTCTTGAGGCACCTCAGAGACCAGAGTCTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_110722550_110723095_2:0:0_4:0:0_117/2 +ATATAGTAAAATATATCATTGTTTGTATCTAAGCCATTATATAGATACGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_185586471_185586808_1:0:0_0:0:0_118/2 +GCTTTCTGGTCTGATTTGACTCTTAGCGAAGGTAAATGTTCACGCACCGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_182936908_182937483_1:0:0_2:0:0_119/2 +CAAGCAGACACATTCATGAGGATTCTATCTGATTCTTCAACTTTTATTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_136882207_136882635_0:0:0_2:0:0_11a/2 +GTTTGGTATTTGAAAATAATGTCTGTGTAATGGATTATGAGAACGGACTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_22027558_22028086_0:0:0_2:0:0_11b/2 +CCCTGGAAGCTCTGTGGAGTCTGGTTGGTTGATATTGTTGTTTTTCCTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_101069088_101069523_0:0:0_0:0:0_11c/2 +CTCCAGCTTGTTTCTTCAGACCTTTTGCTTGGAAAATTGTTTTCCAGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_133430180_133430643_0:0:0_3:0:0_11d/2 +CCTGAGATCCTGTCACTTGATCTGAAGTTTTGCCTTCTGTCTCCCCTGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_141505317_141505766_0:0:0_2:0:0_11e/2 +TTATATGCCCCAGTACAGGGGAACACCAGGGTCAAAAATTGGGAATGGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_103387516_103388014_1:0:0_1:0:0_11f/2 +ATGATTTCCCTACCTGATGAAGGCTTACTTCTTTCTTCACCTTATTTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_134753416_134753860_0:0:0_1:0:0_120/2 +GGACCTGGGCTTAGGGGACAGCAGCAGTCTGACCTCGGCAACAGGGAGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_168048225_168048764_3:0:0_0:0:0_121/2 +CTATCATGATCACATTACCCTTACATCACCATCATCACGAGCCCATCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_15110325_15110842_0:0:0_1:0:0_122/2 +TATGGTTGTATTAAAGTTGACTAATATTAAGAGCTTAAATAGATTTAAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_71511848_71512298_1:0:0_1:0:0_123/2 +GCTTATTAATCCTCTTCTCTTCTTGTATAAAGGGTGGGAAGTAGGTGAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_37275066_37275622_2:0:0_0:0:0_124/2 +GCTGGTTTCCAAATCACAGAGACCTCTCCTGCCTCTACTTCCTGAATCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_191970326_191970894_1:0:0_0:0:0_125/2 +TCGTTAAGAGTAACCAGGGCTCTTAACTGCTGAGCCATCTCTTAGACTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_137258018_137258449_1:0:0_1:0:0_126/2 +TATTGTGAAGTGTTATGTCTGATTGGCTTTTTCTCTTCTTCGGTGAGACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_163885263_163885763_1:0:0_0:0:0_127/2 +TGCAAACCCTTTCAGCTCCTTGGGTACATTCTCTAGCTCCTTCATTGGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_95122061_95122611_1:0:0_2:0:0_128/2 +ATCATCATAGGTGGGCAAAGGAAAGTGTGAAATAGTATAATTTCATGGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_191245641_191246131_1:0:0_1:0:0_129/2 +TTCTTGAGAGAGGCCAGGCTTTGGGGAACAGATGTCGCACAGCACTAAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_11721955_11722368_1:0:0_3:0:0_12a/2 +GGGTTGGAGATCCCTTTAGCTCCTTGGGTGGTTTCCCTAGCACCTCCATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_102954712_102955237_1:0:0_1:0:0_12b/2 +AAGTGGTGTAACCCAATCACAAAAGTACATACAGGATATACACTCACTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_26914346_26914925_0:0:0_1:0:0_12c/2 +AAGGGGAAAAAAAACCCTGCATCTGATATGCAAAGACCAGTCAGAATAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_151053369_151053909_1:0:0_0:0:0_12d/2 +TCTTCTGTCTTGAAAAAGAAAAAGAACACACCACACCCACACACCACACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_93621447_93621970_1:1:0_1:0:0_12e/2 +CATTAAGTGTTAGTTTTAATAGCGCATTGAAAACCCTACCATTTCAATAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_13530953_13531445_0:0:0_0:0:0_12f/2 +GAGTTCATTAGTACATTGGTTGTTTGGAACACAGAAAATCTTTCCCCATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_154530120_154530631_2:0:0_4:0:0_130/2 +AGGCTTTACTTAATCCAAAGCATAAGTACATTGTTTGACACCCTGCAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_100109085_100109588_0:0:0_2:0:0_131/2 +TCACAGAGGACACTCACAGAGATGAACCATGCTCCCAGGGACAAGATGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_150348101_150348543_0:0:0_0:0:0_132/2 +ATTAAACCTGCTGAGTTATTTGAATTCCAGAGACTTACATAATAAACTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_8725925_8726392_0:0:0_3:1:0_133/2 +TATTCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATCATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_189147844_189148204_2:0:0_1:0:0_134/2 +TTAAGACATATTAATTTTAGGAAGTAAAAATAAATTCATTTAAATTGGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_45618673_45619149_2:0:0_2:0:0_135/2 +CTGGATGTCGCTTGTGCAGATCTTGAAAATTTTGTCATAATTGCTGGGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_104062147_104062721_1:0:0_0:0:0_136/2 +ACAAAAACAAGTCAGATAAGGCAGTCCTCTGGTACATATATAAGAAGAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_138405158_138405766_1:1:0_1:0:0_137/2 +CAGGAGGAGCAGGGACGGTCTCTGACGCTGTTGCCTGCCTCTAGATCCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_115548969_115549503_0:0:0_1:0:0_138/2 +TACTCTGTTATCTATGCAGACCAGAGCCTAGCATAATTGTTCTCTGAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_195151172_195151687_0:0:0_0:0:1_139/2 +TTTATCAATACACTCAGCTTTCTAGGCAGAGATTTTTAGGATCAAATGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_138103424_138103925_0:0:0_0:0:0_13a/2 +TCTTAAGCAGCATGTTATTAGACAGAAGTAACAATAACATAAAAGTAACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_84481564_84482032_1:0:0_0:0:0_13b/2 +CCCCAATCCCCCACCCACCGACTCCCCCTTTTTGGCCCTGGCATTCCCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_180211651_180212100_2:0:0_1:0:0_13c/2 +AAAAGGACCCAGCCTGCTCCTGCATCCACTGACTTCCTACTTTGCGTTGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_19484875_19485375_1:0:0_0:0:0_13d/2 +TGTCTCAGTAACTCCCTCCATGGGTATTTTGTTGACCATTCTAACAAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_8815773_8816268_0:0:0_1:0:0_13e/2 +TCAGATATTCTGAGAAGTTTGGGATTTCAGGCATGAAGTCCAGGAAAGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_118367902_118368405_1:0:0_0:0:0_13f/2 +GATTTCAGACTGTAAGTCATTTCAATAAAGTGTTTAATATAGAGAGACAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_83281820_83282310_2:0:0_3:0:0_140/2 +TGAGGGCTCTAAATCACAAATTCACTAGGATTAGACCAGACTAGTGCCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_24810903_24811377_2:0:0_0:0:0_141/2 +AATCGGATAGGGGACTAATATCCAATCTATATAAAGAACTGAAGAATGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_24847990_24848482_1:0:0_1:0:0_142/2 +CCCTTTATGTGACTCTATCACATATATCATTCTCATCATCAGCTTGGAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_25453923_25454484_1:0:0_2:0:0_143/2 +TTTTTATTTTGTTTTGTTCTTGATTGTTTGATTGTTTGTTTGTTTGAGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_35396075_35396608_0:0:0_1:0:0_144/2 +AGGATGACAGTCATACTCAGACCACCATGGCACAAGCCTAGAGACCAGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_184356181_184356676_1:0:0_1:0:0_145/2 +CCTGGCTGGCCAGTGAGACCCAGGATCAATCCATCTCTGCCTTCCCCAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_87890172_87890679_0:0:0_1:0:0_146/2 +TGAGGTGCAAGCATCTGTGTATATGAGTAAAGACCAGAAAGGAGTCTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_192825121_192825655_0:0:0_3:2:0_147/2 +TTTGTTTCTTTCTTTTTTTCTTTCTTTCTTGCTTCCTTCCCTCCTTCCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_29477154_29477657_0:0:0_0:0:0_148/2 +AATGACAGCATCTTCAATAAATGGTGCTGGCACAACTGGCAGTTATCATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_68360607_68361138_2:1:0_2:0:0_149/2 +GGTCATGTCCTCTTTCTCCGTTGAAGAGGAGGGAATCCGTGTGGGGGAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_90679374_90679891_2:0:0_4:0:0_14a/2 +AGTGGGAACATCTGGACCCTTGGCTCCGTAGGCTTATCCCCTTGACAGGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_90921852_90922384_0:0:0_1:0:0_14b/2 +AGGTAGATCTTGGATCGGGAGTTGGGGAGAGTGAGGTGCACTAGCTGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_144744406_144744790_0:0:0_3:0:0_14c/2 +AGTCTGGCGGTTTCTCAGAAAACTGGACATAGTACTACCGGAGGATCCAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_157579434_157579959_0:0:0_1:0:0_14d/2 +AGCCAAATGGATGGACCTGGAGGGCATCATCCTGAGTGAGGTAACACAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_22354013_22354577_0:0:0_2:0:0_14e/2 +TCTTGAGTTCAAGGCCAGACTGGTCCACAGAACTAGTTATAAGACAGCCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_14011029_14011557_0:0:0_1:0:0_14f/2 +CCACCACAAGACTTCGCTACTAAGTCCGAAAATGAGAATGTGCTATTAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130418472_130418955_2:0:0_2:0:0_150/2 +GGAGTCTGGTGACTCAATCTCTGGATTTCACACCTGCAATAAACCAGCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_150912771_150913298_1:0:0_0:0:0_151/2 +GAGACTATGCTGGGGCCTAGCAAACACAGAAGTGGATGCTCACCGTCAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_122600000_122600452_0:0:0_0:0:0_152/2 +AATTTCTAAAATATATAAAATTGTATAATATGATAGAAATGCATATTTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_172852130_172852552_1:0:0_2:0:0_153/2 +TAGCTGAGTAGTACTCCATTGTGTAGATGTACGACATTTTCTGTATCCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_58219252_58219809_1:0:0_1:0:0_154/2 +CTCTCTTTGCTTTCAAATTTATGGACTCCATTCTTGTTAATTACTGTTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_154116562_154116985_0:0:0_0:0:0_155/2 +TTTTTTTAGCTGCTAGGCTTTTGTCTCAGATCAGGATGGTGAGAAAGAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_169424620_169425179_1:0:0_0:0:0_156/2 +TGGCATGAAATGAATGAAAAAAGAAAAAAAGAGAGAGAGAGAAAGAGAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_72776580_72777093_1:0:0_0:0:0_157/2 +TGAGCAGGCCTAGATTCAGTAAATGGATGGATGACTAAATGGATGGGTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_102420738_102421205_2:0:0_1:0:0_158/2 +GGACATTTTCAAAATATCACAGAAGCAAGAAGGACCAAAAGCATAGATTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_148315363_148315906_2:0:0_0:0:0_159/2 +AAATGCCATCCTAACAAAAGAAATCTACAGATTCCATTCAATCCTCATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_93257911_93258453_0:0:0_1:0:0_15a/2 +CTCAGCTTTCCAATGATTGAAACAAGCTTAGACTCTGACATAGGCCCATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_94169994_94170446_0:0:0_1:0:0_15b/2 +AGGGCAGGAAGAGTGTTCTGTGTGTGGAACCTGGTGGCTGGAGGGCCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_126263407_126263894_2:0:0_2:0:0_15c/2 +TGTAATGACCGTTATGTGAGCAGCTGGGGAGAAAAGGCAGGTTGTTTGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_42763327_42763896_1:0:0_0:0:0_15d/2 +AGCCAGTATCCTTTACCTATAAATACCAAAATAAATAAATAAATAAATAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_127932894_127933379_0:0:0_2:0:0_15e/2 +TAAAATACTCACATGCAATGCTGGTGAGGATACCCATCCATCCTATCGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_83608654_83609158_1:0:0_3:0:0_15f/2 +TCCCCTACCCACCCACCACTCCTGTCTTCCCAGCCTGGCATTCTGCTACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_47669914_47670464_0:0:0_0:0:0_160/2 +TGGTGTTAGGCTCTTGTGCATCTTGAGAGAGTTTAAGAAATGGAGTACCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_133731323_133731869_1:0:0_2:0:0_161/2 +TTTTTTTTTTAACGATTTATTTATTGATTATATGTAAGTACACTGTAGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_133255321_133255920_0:0:0_1:0:0_162/2 +CTCACTGTCCTCTGTGCTTTAGGATTCTTGCAAGGCCTTTTGAAGTTCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_23328420_23328852_0:0:0_1:0:0_163/2 +ACTCAGGACCTCTGGAAGAGCAGTTGGTACTCTTAACAGCTGAGCCATCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_53072730_53073291_2:0:0_0:0:0_164/2 +CTGCACGCCCATGTTTATTACAGCATTATACCAAGAACAGCAAAGTAATG ++ +22222222222222222222222222222222222222222222222222 +@chr1_173130259_173130757_3:0:0_2:0:0_165/2 +CATGCTCTCACTAGTCCAGGCTCTGGCCATATACAGGCTGCCATTTTGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_87397192_87397710_2:0:0_1:0:0_166/2 +AATTTTCTGCTCAATCTAGCAAATAAGACATTTTATCAAGAAACTATATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_187438711_187439219_1:0:0_1:0:0_167/2 +GAAAAGGGGATGGGTGATGGAAAATGGGGAAGAGGCTGTGTGAGGGGGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_123461089_123461580_0:0:0_1:0:0_168/2 +CAAAATGAAATCTCTATCACAGAGACTTGATGCTACAATCCTCCCCAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_181088135_181088642_2:0:0_2:0:0_169/2 +AATCGGGCTTCCAGTTACAAAGTCAGCATGACTCCCTTTTTTGGGAGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_167764494_167764902_0:0:0_1:0:0_16a/2 +CCCACCTTCCCCATCTACCCGAGCTCACTATGAGGAGTGCCAGGTTTGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_157283727_157284210_1:0:0_0:0:0_16b/2 +ACTTCTTTCTAAATCATTGACAGAACCAGTTCCAAATGTACGATAGGTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_156428357_156428913_4:0:0_3:0:0_16c/2 +TATAGAAAACACTAAACCCCTAACTTTGTCGACAAATAATAAGTAACCTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_27945156_27945679_0:0:0_2:0:0_16d/2 +TGGACTCATCTATACTCTCCATTTTCTATTTTTTAAATTATTTTAATTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_190959090_190959565_0:0:0_0:0:0_16e/2 +CACTTTCTCTTAGTGTCTCCACGGGCTCTGGAGGGACAGGGACAAGTGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_163184140_163184589_0:0:0_1:0:0_16f/2 +ACAGAACCGACACACAATTCAAACCAGGTTAATTGGTAAGATGTGGGGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_104189461_104189906_1:0:0_1:0:0_170/2 +CCTGCAAGATTGATTTCTGAAGGGTTGTGTTACTTTTCACATCCACTAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_77562742_77563170_2:0:0_0:0:0_171/2 +TACACGTCACTTTTTTAGACAGACATGGGAAATGAACTTCCTTTTTATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_192763088_192763581_0:0:0_0:0:0_172/2 +GGGAGCTGCTGAGATCTACGGTTAAAAACATTTTCTATTCATGAAATTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_36839841_36840369_1:0:0_1:0:0_173/2 +GGCAAAGTAGTAGTAAGTAGGGGCACTGTGATACTTGTTTTATCATAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_114603035_114603542_0:0:0_0:0:0_174/2 +ACGTTCATTTTCAATTAACTCTTGTTTACTCATCAAGGTTCTGGTAACCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_57790506_57791066_2:0:0_0:0:0_175/2 +GTTGGTAAAGAAGTTCTGTCAGGACCTGAAACTTTCCTGCTTACTGGGAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_35650713_35651282_0:0:0_0:0:0_176/2 +AACTGAGAGATGTATTCATCTGGCTGCTTTCCGCTGAGTCGGGGCAAAGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_9711969_9712380_0:0:0_3:0:0_177/2 +ACAGTTGATGCCCTCTTCTGGCCTCTGCAGGCACATATATGATGCACAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_89016556_89017046_1:0:0_0:0:0_178/2 +CTGGTGGTTCACTGTCAAGAAACTAGATGGATTGTGACACATGTGATCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_132197564_132198148_2:0:0_2:0:0_179/2 +AGTTTGAGAACCACTTGATTAGAAAATGGTGTAACTCCCTGCACCAATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_104335733_104336245_1:0:0_3:0:0_17a/2 +AATACCAAATAGAAAAATGTGAGGCATTATAAAGCCAATTAATGCACATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_75633066_75633602_2:0:0_1:0:0_17b/2 +GTACCTTTGGATGGTATAGTAATCAGGAGCTCTCCAAAGGACAAGAACTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_189869166_189869657_0:0:0_1:0:0_17c/2 +CTACCTGAGTTTGGTCCCCAGGACACGCACAAATAAATGTCATAAATTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_27940779_27941192_2:0:0_0:0:0_17d/2 +TGTCTATGTGCTCTGGTTAGGACTTCACATACTATATGGAATAGATAGGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_116796056_116796571_1:0:0_1:0:0_17e/2 +ATATGTACTTCCTGAAGTGGTCCTCTGGCTTCTATTATTTTGCAAAACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_20487571_20488054_3:0:0_1:0:0_17f/2 +TGGGGTGCCCATGACTAGGTGGGGTGGGAGTGCTGCGTTCTGATGATGGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_70106451_70106893_0:0:0_2:0:0_180/2 +CTTTCTTTTTTTCATTTATTAGATATTTTCTTTATATACATTTCAAATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_138350547_138351128_3:0:0_0:0:0_181/2 +GTTTAGTATCACGTGCACACACGGGCCCACCCATAAGTGTAATACATATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_103571822_103572343_2:0:0_1:0:0_182/2 +TTCTGCTAAACTACTATCTACAGAAACAATTAAGGAAATGGGCAACTATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_185391115_185391738_5:0:0_0:0:0_183/2 +TGGGTGTCCTGCGTAGCAAACAGGGTGTTGGTGCTTACCGCAGCTTTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_121389447_121389902_0:0:0_0:0:0_184/2 +GCTGCATGTGTGAGGATTTTTTTAAAAAAAGATTTATTTGTATTTGTATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_44088278_44088819_1:0:0_1:0:0_185/2 +TTTTATTTTTCTGAGAGTTTTCACACATGCACTCAGAATGCTCACACAAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_57600248_57600747_0:0:0_3:0:0_186/2 +TTAATGGTTTCCTTTGTACAGCATCCATTAGTGCCATTGAGGCTGTTCTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_105765709_105766274_0:0:0_4:0:0_187/2 +CCATCACCTAGTCCGTATCACAGAGATACAGAGTGAAATACGTTGTCTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_158039847_158040318_0:0:0_1:0:0_188/2 +TCACATCTAGATTCAGCTGGCAGTCCAGGCTTCAGCTCCACTCACATTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_100649250_100649781_0:0:0_0:0:0_189/2 +TAGAATGGGGATCCTGGAGAGAAGGTTCAGTGGTTGCAAGCACCTTTTTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_92627120_92627576_1:0:0_1:0:0_18a/2 +TCTAACCCAACTGACTAAAATCCGTGCTGTCCGTACAGATGTGGGTAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_47045474_47045999_2:0:0_2:0:0_18b/2 +CACAACAAGATGCAGTTGTATTGTTATGGTGAGGCCAGCAGAGATGACTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_58859721_58860237_3:0:0_1:0:0_18c/2 +TCAGCAAATTGTACGTGCAGAGCGAGGTAACATCAGTTCTGAGGGGCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_38899259_38899748_1:0:0_2:0:0_18d/2 +AGCTGCAGAGAACTCACAAGGAATATGCCAATGTGGCCTTGGCTGGATCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_43169971_43170448_3:0:0_0:0:0_18e/2 +GAACTCAGGACTGATGGCAAACTAAGGAGCGATGGTAACTTTCTGTCACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_169159076_169159522_0:0:0_2:0:0_18f/2 +GTCTTTGTATGCAGTTAGGCCCCCAACTCATAGAGACCTGCCCCTAGTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_14622737_14623201_1:0:0_0:0:0_190/2 +TTGATCAGTAATTGAGAAACTGCCTTACAGTTGGATCTCATGGAGGCATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26821729_26822157_1:0:0_3:0:0_191/2 +GATTTTTTAGTAGGGTTTTATTTCAGTGAAGAGGCACGATGACAAGGGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_146737011_146737509_0:0:0_0:0:0_192/2 +AGGGAATCTTAGTCTGTGTTGTAGACTACAGACGTATCTGCACTCACACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_132937628_132938130_1:0:0_0:0:0_193/2 +CAGGAGCTGTATCTCAACCATAACCAGCTCTGCCGCATCTCCCCCAGGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_108674541_108675003_0:0:0_0:0:0_194/2 +GTTTATATAAGGCCTGCCCTTTGCTGGAGCAAAAGAAGGAGGATGAATGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_155314929_155315340_1:0:0_2:0:0_195/2 +AATAAAATGGCTGTAGGAATTCTGATAGGGATTTCATGAAATGTGTAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_76995369_76995845_0:0:0_0:0:0_196/2 +AGGGTTGTTTTGATTTGCATTTCTCTGATGATTAAGGATGCTGAGCATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_88758655_88759125_1:0:0_1:0:0_197/2 +GTTGTTGTCCTGGGCGGGTGATGATGTTTAATGCCGGGAGAGGAGGAGTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_179447008_179447452_1:0:0_1:0:0_198/2 +TGGGATGCGTACCACAGGTCAGAGGACAACTTGTGGAGGCCAGTTCACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_70539778_70540384_1:0:0_0:0:0_199/2 +TACCAATTCTGAATTATGTAGCTTTTATGTATCTCATTATTATAAATAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_171297998_171298490_3:0:0_2:0:0_19a/2 +ATAACTTTGATCTGAACCAACCACCGGACAGCACTTCCAGCACGTTAGTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_4703882_4704398_1:0:0_1:0:0_19b/2 +AAATGATGCTTTTGGGTTGTTTTGGACCCTCTCCATAATGTTTAAATGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_148373552_148374029_0:0:0_2:0:0_19c/2 +ACAGTAGGCTGTGAATATAATTGTTTTTCACCTTCAGGAAAAGGCTAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_165037832_165038374_1:0:0_2:0:0_19d/2 +CACAGGCTGGAGTTATCACAGAGACAGGAGCTTCAGTTGGGGAAATGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117911191_117911633_0:0:0_2:0:0_19e/2 +GCTTCTGGCTATTATAAATAGGGCTGCTATGGATATAGTGGAGCATTTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_101942751_101943298_2:0:0_2:0:0_19f/2 +GCGAAGGAAATAGATACTAGCCACATTGCCCTGGCGCCATGTAGACAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_159291114_159291545_1:0:0_0:0:0_1a0/2 +AACACCCCCACCCCCCCCACCCCCCCGCACGTTTATGGTGCTCGGTTGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_26628880_26629394_1:0:0_1:0:0_1a1/2 +TAGGCGTTCCCTCATGCTCCTGGAACTCTGGGTCCTGTTGAAGTTACCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_18997387_18997869_1:0:0_1:0:0_1a2/2 +AAGCAAAATTGGAAAACTAGTTTGGGAATTCCAGAGTAGTATTGGTATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_39575593_39576071_1:0:0_2:0:0_1a3/2 +GGAAGCTAGGATCTCTCAGGAGCCTTGTGGAAAGATGGTGTGTGGACAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_5509844_5510306_2:0:0_1:0:0_1a4/2 +ACACAGCTGGAGTTATGTCAGAGAAAGGAGCTTCATTTGAGGAAATGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_109704460_109704956_1:0:0_0:0:0_1a5/2 +GTATTCAACAAATGAAAGAAATACACTAATAACATTATTTTTACTATGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_156587931_156588493_1:0:0_1:0:0_1a6/2 +CGCTGACTCCAGAAGCTACTGGCAGTGGCTGCTGGGAGAGAGAGTCACTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_176610586_176611106_1:0:0_0:0:0_1a7/2 +CTTTTGCAATGTGATTAAAAGAAATGCCATCCATTTCCATGTTTTTAAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_180872448_180872981_1:0:0_3:0:0_1a8/2 +GGCTTCACCAATAGCTTCTCACAGGCTCTCTTCATGGTGTGAAGCCTCAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_26474215_26474717_2:0:0_1:0:0_1a9/2 +GTCCTCTGATCATTTCTGCACATGGAGCGGTTCTGAGATTGGCGGATGGC ++ +22222222222222222222222222222222222222222222222222 +@chr1_104541278_104541749_1:0:0_0:0:0_1aa/2 +GATTTTTATTTTATTTTATTTTATTTTTTGATTGGATATTTTCTTCATTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_67015960_67016373_2:0:0_1:0:0_1ab/2 +ACACCCAGACCAACATTTTTGTCAATAAAATAAAACCCTGTCCTCTATTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_29940243_29940732_0:0:0_1:0:0_1ac/2 +GTTTCATTCCAGGGATGCAGGAATTGTTTAATATATGGAAATCCATCAAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_193079402_193079850_1:0:0_6:0:0_1ad/2 +TCCAGCTCAAAACATCATCAGAAACAGAGTCTACGACTGAAACTGCTTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_117439972_117440528_1:0:0_0:0:0_1ae/2 +AAAATCTGCCCAACTAGATTAGAGAAATTATCTCAATATTCTAACCTTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_177239334_177239795_2:0:0_1:0:0_1af/2 +GGGTACTGGTTAGTTCATAATGTTTTTCCACCTATAGGGTTGCAGATCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_158414545_158415096_3:0:0_0:0:0_1b0/2 +TATCTATCACGAGTGTATAATCTCAAGCCCTCGTCCTAATTTTGAAACAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_97093485_97093964_1:0:0_0:0:0_1b1/2 +GGTCCAACTAAAGAAAGATGTCTCTGATATCACATTCCTGGTGCTTCAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_67614138_67614777_0:0:0_0:0:0_1b2/2 +TTATTGCTCATCCTGAATATGAGCACACACACACACACACATACACATAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_153549562_153550076_0:0:0_1:0:0_1b3/2 +GGCAGGACTGGAGCAGTAGTGTCAGTCTAGAGCGCCAAGTGGCTGCTAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_55425424_55425904_0:1:0_0:0:0_1b4/2 +AAGAATCCAGACAGATGAAAGTTTTTTTTTCTTATTAAAGAATTACCTGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_191019412_191019908_2:0:0_1:0:0_1b5/2 +GTGTGCACACTGCTGAAAAAGGACGCGTTTCTCTTACTGTTTTCGTACCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_73180421_73180945_2:0:0_2:0:0_1b6/2 +CTTGAGTTCTTTCTATATATTGGATCTGTTCTTAAGAGCTGTCTCATTTC ++ +22222222222222222222222222222222222222222222222222 +@chr1_38129466_38129932_2:0:0_2:0:0_1b7/2 +CGGGCGGCAGCTTGGTGATGCGGCGGGTCCCGCGCCACCTCCGCCCAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_133540103_133540570_0:0:0_0:0:0_1b8/2 +CACACACACACACACACACACACACACACGCTTGTGCACATACGTGCTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_184916633_184917139_2:0:0_2:0:0_1b9/2 +AAAGAGAAGATCTTGTGGATGGAAATCAAGGCTGCTCTGTCCAGGTAACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_175669652_175670114_1:0:0_1:0:0_1ba/2 +CAGGGATCCCAAAAGTGTGGTTCCATTTTACAACACAGCTTTGAGTACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_8296849_8297319_1:0:0_0:0:0_1bb/2 +GAATTTGAATAACTACTCATTTACATAAGACATCACAACATTACAGTAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_152905590_152906078_1:0:0_1:0:0_1bc/2 +AGTAAACATCAAAGACAAGTCATCAGTGAACAGGCCAACGAGCGGGAGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_114902352_114902833_0:0:0_0:0:0_1bd/2 +CCATGGAAGGAGTTACAGAGATAAAGTTTGGAGCTGTGATGAAAGGATGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_192964279_192964734_0:0:0_0:0:0_1be/2 +TCTGAAGAGAATGTTCAAAGTTTCATTTCATTTTTATAACTTCTGACATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_38321189_38321768_1:0:0_3:0:0_1bf/2 +TGTCCAAACTGAGCTCAAAAGCCTCCTCTGTAGCTGCTTGAAGGAGATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_78900626_78901065_0:0:0_0:0:0_1c0/2 +TCAATTTACTTCTCTTTGACTGCCTTGTGCTTCCAAAGAAACCAGAAAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_113540760_113541176_0:0:0_3:0:0_1c1/2 +GTACATACTAAAGTTGAATGTGTCAGGCAAATAAATTGAGAGACTATAAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_130677359_130677835_0:0:0_1:0:0_1c2/2 +AACACTGCCTTTTCATTTCTAAGGAGTCTTTTCTTTCTTACTTTTTTTCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_180204210_180204758_2:0:0_0:0:0_1c3/2 +TATAGATATTTTAAGCCAACAACAAAGCTATTCTGGCGAGGGATCACATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_192984278_192984850_2:0:0_5:0:0_1c4/2 +ATATGGAGTGTGAAAAGATGTCAATGGACATAAAGCAAGTGATCTGAGTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_176155520_176156071_0:0:0_4:0:0_1c5/2 +GGCCGATTCTCTACTCTAACAGAATGACAGTGTGTCAGAAGGATCCAAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_11299746_11300227_3:0:0_1:0:0_1c6/2 +TACTCATACAACAGATAAAGGCAGTGGAATCCTTAAGACAGGTTTTAACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_40475921_40476533_1:0:0_0:0:0_1c7/2 +GCTGGTTTTCTTTCCTTTTCAAAAGATGTTAGGTTTTAAGATTCTGTGTG ++ +22222222222222222222222222222222222222222222222222 +@chr1_161162459_161162939_0:0:0_0:1:0_1c8/2 +TGTGCATGAGTGTCAACGTGTGTGTGTGTGTGTGTGTGTGTGTGTACCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_56968239_56968712_1:0:0_4:0:0_1c9/2 +TCAACTTGGTGATACAGTCCGACCACCCATTCCCCCATCCCTTATGTCCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_90357627_90358090_2:0:0_1:0:0_1ca/2 +ACACATACCATCTACCAAAGACATGTATACACATACACCACACACCACAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_184900782_184901265_1:0:0_1:0:0_1cb/2 +GAGCGAGCACTGGCACCTGCGGCTCACCTGGCTGTGTCGGCTCTGCCGCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_34520052_34520514_0:0:0_0:0:0_1cc/2 +AGAGAGGTGGGAGGGAAATAAGAAGAGAGTGGGGCAGGAGCAGGAGCAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_121381246_121381739_0:0:0_0:0:0_1cd/2 +TGCTATCCAGATGTAAAGTGAATAAATAAATGAAAAAATTGAAAAAAAAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_80355344_80355825_1:0:0_3:0:0_1ce/2 +GCTAACCAAATCCAAGAACACATCAAAAGAATTATCCATCCTGACCAAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_23025664_23026100_0:0:0_2:0:0_1cf/2 +GAGTATGGTGCCACTATGTCTTGCTACTATAAATTTCAACTCAAAGCAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_126877190_126877687_2:0:0_0:0:0_1d0/2 +AGAGTTCAAGCCTTTGTCCATTTCTCAACAGGAAACAGACAGGACCTTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_64317525_64318044_1:0:0_0:0:0_1d1/2 +GGCCCGCTTTCTATTTATTTGTTTGTTTGTTTATTTATTTATTTATTTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_41387597_41388152_2:0:0_4:0:0_1d2/2 +TTCATAATGGAGAATTCAAAGGAACATGAGAGGTAGAAATATTTCTAAGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_179273458_179273967_4:0:0_2:0:0_1d3/2 +ACTCTGGAGGCCACACCTTGATGTCTGGTGTTTTCCTCACACTCTCCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_159718146_159718573_1:0:0_1:0:0_1d4/2 +ACTCTAGTCAATATCATCTATGGAAACTGACTCATTTCCCTTAACCTACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_77989741_77990190_3:0:0_2:0:0_1d5/2 +AGGGTATCATCCTGAGTGAGGTAACCCAATCAGAAAGGAACTCGCACCAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_70921539_70922106_2:0:0_0:1:0_1d6/2 +GTCAGTATATGATATTTCCTCAGTCTGTCAAATACTCCATGTCAGCGTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_135807545_135808030_2:1:0_0:0:0_1d7/2 +AAGGTAGAGGTGGTGGCTGAGGAGCGCAATGATCTTGAAGCCAAATGCCT ++ +22222222222222222222222222222222222222222222222222 +@chr1_140999216_140999698_1:0:0_1:0:0_1d8/2 +TCCTCCATGGATGGGCTTGAGAAAGGACCCAAGACTAAACCACCAAAGAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_148512883_148513388_0:0:0_1:0:0_1d9/2 +CTCTCTTTCCACTGATGGCTGACTAGGACATCTTCTGATACATATGCACC ++ +22222222222222222222222222222222222222222222222222 +@chr1_95472009_95472435_1:0:0_0:0:0_1da/2 +GGTTGCCTTTGTCCAGCTTTTATATGAGGGCTGTGTGCCTAGTCCTAATT ++ +22222222222222222222222222222222222222222222222222 +@chr1_19217196_19217734_0:0:0_1:0:0_1db/2 +TGTGTGTGTGTTTGTGTGTGTGTGTGTACACGTGTGCACGCGCGTCTTGG ++ +22222222222222222222222222222222222222222222222222 +@chr1_4075909_4076300_0:0:0_1:0:0_1dc/2 +AAATTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTTCCTATTCTCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_186978576_186979074_1:0:0_0:0:0_1dd/2 +CAGAACAAACCAGAGCCCCGTTCATTGTTTTCTGTGGCTTTTGCTATGAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_112188833_112189331_0:0:0_1:0:0_1de/2 +TTCAACCTACTACAACTCCCAAATGAATTCCAAAGCATTCCATTGCTTAA ++ +22222222222222222222222222222222222222222222222222 +@chr1_173609986_173610514_0:0:0_0:0:0_1df/2 +TGCTCAAGAAACAAAGGTGGGACAGTGAAAAAACAACTGGATAAAAGCTT ++ +22222222222222222222222222222222222222222222222222 +@chr1_22017871_22018438_0:0:0_2:0:0_1e0/2 +AGTTCTTAATTTAATAGACTCAGTACATCTTTAGAGTGCCTTGTTTTAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_48541209_48541729_1:0:0_2:0:0_1e1/2 +CGACCCATACAAAGATGTATGAATCTCACTTAGGAAGGTGAATAAAATAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_10384181_10384617_2:0:0_0:0:0_1e2/2 +CGAGACATGATAATCAGAACAACAAATGGACTAAATAAAGATAGAATACT ++ +22222222222222222222222222222222222222222222222222 +@chr1_20392227_20392827_2:0:0_0:0:0_1e3/2 +CCCTGACTAAGACACTCTGCTATGCTTGCAGACAGGCGCATGTTGTCCAC ++ +22222222222222222222222222222222222222222222222222 +@chr1_171278949_171279483_0:0:0_0:0:0_1e4/2 +TGTTGAGCAAAGAAGCCCCCCTCCTCCCCCCGAAGGCCTATTTTGCTATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_58815142_58815652_3:0:0_0:0:0_1e5/2 +GGGGACCCAGTGTGGGTTCCTCAATGGCACCTATCCTCTGAAAAACTAGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_157206264_157206747_1:0:0_3:0:0_1e6/2 +AAAGATTAAATTGTATGTACATTATTCTCTTTCATTCTCTCTTAGATATC ++ +22222222222222222222222222222222222222222222222222 +@chr1_130727486_130727887_0:0:0_1:0:0_1e7/2 +TCCAGATAACCCAACAGAAAAGGGATTTATCCCAGTTATTGATGAAGATA ++ +22222222222222222222222222222222222222222222222222 +@chr1_56227774_56228368_1:0:0_2:0:0_1e8/2 +GGTCTTTCATTGGGCTTCTTCCACTAAAGGAAACATGAGAAGAGTGGACA ++ +22222222222222222222222222222222222222222222222222 +@chr1_163976865_163977422_1:0:0_2:0:0_1e9/2 +GGAGTGTTTTTATTGACAGGTGTTAGTGCTTTTATAAAAAAAAACTATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_75768405_75768873_1:0:0_0:0:0_1ea/2 +TGTTGTGAAACCTGAAGATGGAGAGAGACAGAGATAGATAAAAGAGACAG ++ +22222222222222222222222222222222222222222222222222 +@chr1_99777250_99777759_1:0:0_0:0:0_1eb/2 +GTACTGTAGACCAAATTAATAAACAACACATACAAATAAATCCAAGAGAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_6944229_6944786_1:0:0_3:0:0_1ec/2 +ACCTGATCTACCATGGAGCTCCAAGTAGGAAGGACAGAACTGATTGGTAT ++ +22222222222222222222222222222222222222222222222222 +@chr1_6751099_6751639_3:0:0_0:0:0_1ed/2 +GAGACTGGGATGTAAAGTGAATAAGTAAACAGAGTATTTCTTGTTTATTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_28492407_28492923_0:0:0_2:0:0_1ee/2 +CCGCATAGTGCCAGTAACAGATGCAAGCTTACAACTTGATCCCCACCTGA ++ +22222222222222222222222222222222222222222222222222 +@chr1_25977449_25977911_3:0:0_0:0:0_1ef/2 +TTTCCCCCCATTCAAGTCTTTTAGTTTGTTCTTGTGAGGCACTGAGTTTA ++ +22222222222222222222222222222222222222222222222222 +@chr1_180012197_180012695_1:0:0_3:0:0_1f0/2 +TGTGTGGAATACGATGACGATAGATGAGGCATTCTGTTTGATTTTCTGCA ++ +22222222222222222222222222222222222222222222222222 +@chr1_139551031_139551593_1:0:0_0:0:0_1f1/2 +ACTAATAGACAACCATTTACTCTGATTCAACTGGCTGCCAATTTCTGAGT ++ +22222222222222222222222222222222222222222222222222 +@chr1_88565594_88566005_0:0:0_1:0:0_1f2/2 +ACAGACAACATGGAGAACATGGGGAGGGGGCAATGAAAAGTATTAAAGCC ++ +22222222222222222222222222222222222222222222222222 +@chr1_28334498_28334996_0:0:0_0:0:0_1f3/2 +GAGGACTCCAAAGGATGTCAAAGACTTCACAGTAAGTACTCTGGGCAGGA ++ +22222222222222222222222222222222222222222222222222 From bda216ecf00a9aba47b13279e7e22cd46ac1f5b5 Mon Sep 17 00:00:00 2001 From: Dave B Date: Fri, 4 May 2018 12:59:59 -0400 Subject: [PATCH 26/35] Fixes per Nicola's advice - Add support for fasta.bz2 - Only add quality offset flag on fastq files - Tokenize the cat command and make it dependent on input format --- .../fasta_formatter/fasta_formatter.xml | 2 +- .../fasta_nucleotide_changer.xml | 2 +- .../fastq_quality_converter.xml | 3 +-- .../fastq_quality_filter.xml | 3 +-- .../fastq_to_fasta/fastq_to_fasta.xml | 7 +++---- .../fastx_artifacts_filter.xml | 3 +-- .../fastx_barcode_splitter.xml | 2 +- .../fastx_clipper/fastx_clipper.xml | 2 +- .../fastx_collapser/fastx_collapser.xml | 3 +-- .../fastx_quality_statistics.xml | 3 +-- .../fastx_renamer/fastx_renamer.xml | 3 +-- .../fastx_reverse_complement.xml | 2 +- .../fastx_trimmer/fastx_trimmer.xml | 3 +-- tool_collections/fastx_toolkit/macros.xml | 17 +++++++++++++---- 14 files changed, 28 insertions(+), 27 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml index 0d717c2797b..66c3b52fd9e 100644 --- a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml +++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml @@ -15,7 +15,7 @@ --> diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml index 18c38aedde6..95237523fa1 100644 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -6,7 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml index 5a21891033a..a0b3e4978e5 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml @@ -6,8 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index 7c7fee285d3..ee02979fc86 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -6,8 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index bd767556de8..f53007a6921 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -5,10 +5,9 @@ - + diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index ff21ccac0f8..59550bea520 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -6,8 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 1cf307c64c6..6f6c02ce8f1 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -6,7 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 7dfd8db5520..0c928832efa 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -6,8 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index fceed713ff0..c9fd3245d86 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -6,8 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index e1f790bd473..5d07fe22b6a 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -6,8 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 97d8b0fbd67..3a0f9d1b27c 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -6,7 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index 1e61d744d6a..5f0c894234a 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -6,8 +6,7 @@ diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml index 98f48d20f56..679a99c19e5 100644 --- a/tool_collections/fastx_toolkit/macros.xml +++ b/tool_collections/fastx_toolkit/macros.xml @@ -1,10 +1,19 @@ + + #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): + zcat -f '$input' | + #elif $input.is_of_type('fasta.bz2'): + bzcat -f '$input' | + #else: + cat '$input' | + #end if + @@ -28,12 +37,12 @@ - + - + \ No newline at end of file From 93a658e3e2e1da64ffbff61ae886c704a10c0410 Mon Sep 17 00:00:00 2001 From: Dave B Date: Fri, 4 May 2018 14:17:23 -0400 Subject: [PATCH 27/35] Support bz2 compressed filetypes that exist. --- tool_collections/fastx_toolkit/macros.xml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml index 679a99c19e5..5b96915489e 100644 --- a/tool_collections/fastx_toolkit/macros.xml +++ b/tool_collections/fastx_toolkit/macros.xml @@ -3,7 +3,7 @@ #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): zcat -f '$input' | - #elif $input.is_of_type('fasta.bz2'): + #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): bzcat -f '$input' | #else: cat '$input' | @@ -11,9 +11,9 @@ @@ -24,6 +24,11 @@ + fastqsanger,fastqsanger.gz,fastqsanger.bz2 + fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2 + fastqillumina,fastqillumina.gz,fastqillumina.bz2 + @SANGER@,@SOLEXA@,@ILLUMINA@ + fasta,fasta.gz @@ -37,12 +42,12 @@ - + - + - + \ No newline at end of file From 9dd5464705a71e80fea87e0d45b7f966e99ddeae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 4 May 2018 22:39:25 +0200 Subject: [PATCH 28/35] style changes --- .../fastq_to_fasta/fastq_to_fasta.xml | 51 ++++++++----------- 1 file changed, 22 insertions(+), 29 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index f53007a6921..e6b86e4f6b9 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -1,42 +1,36 @@ - converter from FASTX-toolkit + converter from FASTX-toolkit macros.xml - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - + + + + + + + + @@ -52,7 +46,6 @@ - **What it does** From 20f8c8eb7efa519ea4380e3033d6ef240ba566ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 4 May 2018 22:42:03 +0200 Subject: [PATCH 29/35] quote script name --- .../fastx_barcode_splitter/fastx_barcode_splitter.xml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 6f6c02ce8f1..33039711b2e 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -6,7 +6,7 @@ '$summary' ]]> - @@ -42,11 +41,8 @@ - - - From bba9ee1126605631ba1f2ac0423f543288f52c54 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 4 May 2018 22:45:07 +0200 Subject: [PATCH 30/35] style fixes --- .../fastx_nucleotides_distribution.xml | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 14c54053aad..a8abc1fcc6d 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,19 +1,21 @@ - + macros.xml - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i '$input' -o '$output' - - - - - - - - - + + fastx_nucleotide_distribution_graph.sh + -t '$input.name' + -i '$input' + -o '$output' + + + + + + + @@ -57,6 +59,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - + From 200ea400662792083305f375dff750a0ddab2a1c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 4 May 2018 22:49:07 +0200 Subject: [PATCH 31/35] small style adjustments --- .../fastx_toolkit/fastx_trimmer/fastx_trimmer.xml | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index 5f0c894234a..b277c6e0503 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -9,17 +9,10 @@ @CATS@ fastx_trimmer -v -f $first -l $last -o '$output' @FQQUAL@ ]]> - - - - - - - - - + + From f9ebaa02a434640c2a2bca045cd8a3d495eaec5c Mon Sep 17 00:00:00 2001 From: Dave B Date: Mon, 7 May 2018 09:30:48 -0400 Subject: [PATCH 32/35] Tabs to spaces, add @VERSION@ token. --- .../fastq_quality_boxplot.xml | 16 +++---- .../fastq_to_fasta/fastq_to_fasta.xml | 46 +++++++++---------- .../fastx_nucleotides_distribution.xml | 16 +++---- tool_collections/fastx_toolkit/macros.xml | 3 +- 4 files changed, 41 insertions(+), 40 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml index 96938abc9f9..da5eac12522 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml @@ -1,18 +1,18 @@ - + macros.xml - fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' + fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' - - - + + + - - - + + + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index f53007a6921..073e9e20db2 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -1,42 +1,42 @@ - converter from FASTX-toolkit + converter from FASTX-toolkit macros.xml - + - + - - + + - - - - + + + + - - - - + + + + - + - - - - - - - - + + + + + + + + @@ -51,7 +51,7 @@ - + diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 14c54053aad..f8769283a2e 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,18 +1,18 @@ - + macros.xml - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i '$input' -o '$output' + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i '$input' -o '$output' - - - + + + - - - + + + diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml index 5b96915489e..89d86f9c5a7 100644 --- a/tool_collections/fastx_toolkit/macros.xml +++ b/tool_collections/fastx_toolkit/macros.xml @@ -20,10 +20,11 @@ - fastx_toolkit + fastx_toolkit + 0.0.14 fastqsanger,fastqsanger.gz,fastqsanger.bz2 fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2 fastqillumina,fastqillumina.gz,fastqillumina.bz2 From 6cb5c84b2d5015ca6e5b2656ce86534e28fe3333 Mon Sep 17 00:00:00 2001 From: Dave B Date: Mon, 7 May 2018 15:51:27 -0400 Subject: [PATCH 33/35] Fix more indentation. --- .../fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml | 6 +++--- .../fastx_nucleotides_distribution.xml | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index e6b86e4f6b9..a15cc2c3990 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -45,8 +45,8 @@ - - + + **What it does** @@ -78,7 +78,7 @@ Will be converted to FASTA (with 'rename sequence names' = YES):: This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - + diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index a8abc1fcc6d..6ae3222cb02 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -22,7 +22,7 @@ - + **What it does** @@ -58,7 +58,7 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - - - + + + From f6e182936e7b316315292420fd32fac9c98661c9 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 8 May 2018 12:02:05 +0100 Subject: [PATCH 34/35] Restore URL linting (fixed in Planemo 0.49.0) --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 728dfa65a2f..c9f20fe2f5c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -29,7 +29,7 @@ jobs: script: - set -e - cd "$TRAVIS_BUILD_DIR" && flake8 --exclude=.git,./deprecated/ . - - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories.list + - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories.list - stage: test env: CHUNK=0 From 60a914f365d8a01e5b495bed7b610380783a9669 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 8 May 2018 13:40:05 +0100 Subject: [PATCH 35/35] More CDATA, indentation fixes. Use element_identifier Attribute order per IUC style. --- .../fasta_clipping_histogram.xml | 14 +++--- .../fasta_formatter/fasta_formatter.xml | 16 +++---- .../fasta_nucleotide_changer.xml | 17 +++---- .../fastq_quality_boxplot.xml | 21 ++++---- .../fastq_quality_converter.xml | 17 +++---- .../fastq_quality_filter.xml | 28 +++++------ .../fastq_to_fasta/fastq_to_fasta.xml | 19 ++++---- .../fastx_artifacts_filter.xml | 17 +++---- .../fastx_barcode_splitter.xml | 48 +++++++++---------- .../fastx_clipper/fastx_clipper.xml | 33 +++++++------ .../fastx_collapser/fastx_collapser.xml | 19 ++++---- .../fastx_nucleotides_distribution.xml | 22 ++++----- .../fastx_quality_statistics.xml | 17 ++++--- .../fastx_renamer/fastx_renamer.xml | 18 +++---- .../fastx_reverse_complement.xml | 15 +++--- .../fastx_trimmer/fastx_trimmer.xml | 19 ++++---- tool_collections/fastx_toolkit/macros.xml | 8 ++-- 17 files changed, 178 insertions(+), 170 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index 3658877906d..ca237fe1e08 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -6,14 +6,18 @@ perl-gdgraph - fasta_clipping_histogram.pl '$input' '$outfile' + - + @@ -25,8 +29,7 @@ - - - + ]]> diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml index 66c3b52fd9e..efaeb6099d9 100644 --- a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml +++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml @@ -13,18 +13,18 @@ So this XML tool only changes the width (line-wrapping) of a FASTA file. --> - - - + - + @@ -40,7 +40,7 @@ - + single line):: This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - + ]]> diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml index 95237523fa1..54424a9eddc 100644 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -4,11 +4,12 @@ macros.xml - - - + @@ -18,7 +19,7 @@ - + @@ -32,7 +33,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml index da5eac12522..9e856f28042 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml @@ -4,14 +4,21 @@ macros.xml - fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' + - + - + @@ -19,8 +26,7 @@ - - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml index a0b3e4978e5..dbfcceedd42 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml @@ -4,11 +4,12 @@ macros.xml - - - + @@ -18,7 +19,7 @@ - + @@ -58,7 +59,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index ee02979fc86..2101eeb6948 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -4,25 +4,25 @@ macros.xml - - - + - - - + - - - + - + @@ -40,7 +40,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index a15cc2c3990..3af86921661 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -4,11 +4,13 @@ macros.xml - - - + @@ -21,7 +23,7 @@ - + @@ -46,8 +48,7 @@ - - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index 59550bea520..d669493ff95 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -4,17 +4,18 @@ macros.xml - - - + - + @@ -28,7 +29,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 33039711b2e..cbb64975b48 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -5,24 +5,23 @@ '$summary' - ]]> - +mkdir split && +@CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE' +--prefix 'split/' +--suffix '.$input.extension' +--mismatches $mismatches +--partial $partial +#if $refBarcodeLocation.barcodeLocation == "idxfile": + --idxfile '$refBarcodeLocation.idxfile' + --idxidstrip $refBarcodeLocation.idxidstrip +#else: + $refBarcodeLocation.EOL +#end if +> '$summary' + ]]> - - + + @@ -37,16 +36,16 @@ - - + + - - + + - + @@ -89,7 +88,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index a2c75308477..c42242c5648 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -4,19 +4,23 @@ macros.xml - - - + ]]> - - - + @@ -38,10 +42,9 @@ - - - use this for hairpin barcoding. keep at 0 unless you know what you're doing. - + @@ -55,7 +58,7 @@ - + @@ -70,7 +73,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 0c928832efa..5c7302e5510 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -4,27 +4,27 @@ macros.xml - - - + - + - + - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 6ae3222cb02..ce3c093ec1d 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -4,17 +4,17 @@ macros.xml - - fastx_nucleotide_distribution_graph.sh - -t '$input.name' - -i '$input' - -o '$output' - + - + - + @@ -22,8 +22,7 @@ - - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index c9fd3245d86..04465918747 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -4,17 +4,17 @@ macros.xml - - - + - + @@ -22,7 +22,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index 5d07fe22b6a..44a3b2030b2 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -4,11 +4,13 @@ macros.xml - - - + @@ -20,7 +22,7 @@ - + @@ -29,7 +31,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 3a0f9d1b27c..547b0c4d99a 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -4,17 +4,16 @@ macros.xml - - - + ]]> - + @@ -28,7 +27,7 @@ - + + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index b277c6e0503..c6d2341f9a4 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -4,18 +4,20 @@ macros.xml - - - + - + @@ -33,7 +35,7 @@ - + 2-1 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA - Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: >1-1 @@ -69,7 +70,7 @@ Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (base This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - + ]]> diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml index 89d86f9c5a7..8e70d9b99d2 100644 --- a/tool_collections/fastx_toolkit/macros.xml +++ b/tool_collections/fastx_toolkit/macros.xml @@ -43,12 +43,12 @@ - + - + - + - \ No newline at end of file +