diff --git a/example_browser/browser_tracks.ini b/example_browser/browser_tracks.ini index d3b9b4e..5c7f855 100644 --- a/example_browser/browser_tracks.ini +++ b/example_browser/browser_tracks.ini @@ -7,32 +7,37 @@ title = Kc DpnII (Li et al. 2015) colormap = RdYlBu_r depth = 200000 transform = log1p -x labels = yes -boundaries_file = domains.bed + +[boundaries] +file = domains.bed +file_type = domains +overlay_previous = share-y +color = None [spacer] -width = 0.05 +height = 0.05 [tad state] file = tad_classification.bed -width = 0.5 +height = 0.5 title = TAD state display = collapsed -labels = off +labels = false [tad-separation score] file = tad_score.gz -width = 10 +height = 10 type = lines title= TAD separation score (Ramirez et al.) file_type = bedgraph_matrix [genes] file = dm3_genes.bed.gz -width = 20 +height = 20 title = genes fontsize = 12 -global max row = yes +global_max_row = true +labels = true [vlines] file = domains.bed diff --git a/hicbrowser/client/js/templates.js b/hicbrowser/client/js/templates.js index c9dbf78..b728f4d 100644 --- a/hicbrowser/client/js/templates.js +++ b/hicbrowser/client/js/templates.js @@ -57,7 +57,7 @@ this["Templates"]["gene"] = Handlebars.template({"1":function(container,depth0,h },"useData":true}); this["Templates"]["index"] = Handlebars.template({"compiler":[7,">= 4.0.0"],"main":function(container,depth0,helpers,partials,data) { - return "
\n
\n
\n

HiCBrowser is a simple web browser to visualize Hi-C and other genomic tracks. \n

It is based on HiCExplorer, a set of programs that enable you to process, normalize, analyze and visualize Hi-C data.

\n
\n
\n \n \"\"\n \n
\n
\n
\n
\n"; + return "
\n
\n
\n

HiCBrowser is a simple web browser to visualize Hi-C and other genomic tracks. \n

It is based on pyGenomeTracks, a program and library to plot beautiful genome browser tracks.

\n
\n
\n \n \"\"\n \n
\n
\n
\n
\n"; },"useData":true}); this["Templates"]["loading"] = Handlebars.template({"compiler":[7,">= 4.0.0"],"main":function(container,depth0,helpers,partials,data) { diff --git a/hicbrowser/client/templates/index.hbs b/hicbrowser/client/templates/index.hbs index c830842..554bb89 100644 --- a/hicbrowser/client/templates/index.hbs +++ b/hicbrowser/client/templates/index.hbs @@ -2,7 +2,7 @@

HiCBrowser is a simple web browser to visualize Hi-C and other genomic tracks. -

It is based on HiCExplorer, a set of programs that enable you to process, normalize, analyze and visualize Hi-C data.

+

It is based on pyGenomeTracks, a program and library to plot beautiful genome browser tracks.

diff --git a/hicbrowser/runBrowser.py b/hicbrowser/runBrowser.py index 721ba56..a6fee90 100644 --- a/hicbrowser/runBrowser.py +++ b/hicbrowser/runBrowser.py @@ -22,7 +22,7 @@ def parse_arguments(args=None): parser.add_argument('--htmlFolder', help='File where the template index.html file is located. The default is' - 'fine unless the contents wants to be personalized. The full path ' + ' fine unless the contents wants to be personalized. The full path ' 'has to be given.', default=None) diff --git a/hicbrowser/static/js/App.js b/hicbrowser/static/js/App.js index 4a40052..314d7d1 100644 --- a/hicbrowser/static/js/App.js +++ b/hicbrowser/static/js/App.js @@ -275,7 +275,7 @@ this["Templates"]["gene"] = Handlebars.template({"1":function(container,depth0,h },"useData":true}); this["Templates"]["index"] = Handlebars.template({"compiler":[7,">= 4.0.0"],"main":function(container,depth0,helpers,partials,data) { - return "
\n
\n
\n

HiCBrowser is a simple web browser to visualize Hi-C and other genomic tracks. \n

It is based on HiCExplorer, a set of programs that enable you to process, normalize, analyze and visualize Hi-C data.

\n
\n
\n \n \"\"\n \n
\n
\n
\n
\n"; + return "
\n
\n
\n

HiCBrowser is a simple web browser to visualize Hi-C and other genomic tracks. \n

It is based on pyGenomeTracks, a program and library to plot beautiful genome browser tracks.

\n
\n
\n \n \"\"\n \n
\n
\n
\n
\n"; },"useData":true}); this["Templates"]["loading"] = Handlebars.template({"compiler":[7,">= 4.0.0"],"main":function(container,depth0,helpers,partials,data) { diff --git a/hicbrowser/static/js/App.min.js b/hicbrowser/static/js/App.min.js index 771565e..ec5cb46 100644 --- a/hicbrowser/static/js/App.min.js +++ b/hicbrowser/static/js/App.min.js @@ -1,4 +1,4 @@ -!function a(b,c,d){function e(g,h){if(!c[g]){if(!b[g]){var i="function"==typeof require&&require;if(!h&&i)return i(g,!0);if(f)return f(g,!0);var j=new Error("Cannot find module '"+g+"'");throw j.code="MODULE_NOT_FOUND",j}var k=c[g]={exports:{}};b[g][0].call(k.exports,function(a){var c=b[g][1][a];return e(c?c:a)},k,k.exports,a,b,c,d)}return c[g].exports}for(var f="function"==typeof require&&require,g=0;g did not match any gene. Check the browser for examples of valid gene names as they may be an id.";App.views.search.renderError(e),d()}})}),j.on("route:getBrowser",function(){return g.isUndefined(i.browser)?(App.views.search.showBrowserView(),void d()):(App.router.navigate("/browser/"+i.browser.id,{trigger:!1}),void f(i.browser))}),j.on("route:getBrowserId",function(a){if(!g.isUndefined(i.browser)&&i.browser.id===a)return void f(i.browser);var b=new App.models.Browser({id:a}),c="Your search - "+a+" - did not match any region.";b.fetch({success:function(a){a=a.toJSON();var b=g.flatten(a.tracks);0===b.length?(App.views.search.renderError(c),d()):$.ajax({url:b[0],success:function(){i.browser=a,f(a)},error:function(){App.views.search.renderError(c),d()}})},error:function(a,b){App.views.search.renderError(c),d()}})}),j.on("route:defaultRoute",d),Backbone.history.start(),b.exports=j},{underscore:82}],6:[function(a,b,c){(function(d){var e="undefined"==typeof window?d:window,f=e.Handlebars||a("handlebars");this.Templates=this.Templates||{},this.Templates.browser=f.template({1:function(a,b,c,d,e){var f=a.lambda,g=a.escapeExpression;return'
\n \n \n
\n'},compiler:[7,">= 4.0.0"],main:function(a,b,c,d,e){var f;return'
\n
\n'+(null!=(f=c.each.call(null!=b?b:{},null!=b?b.tracks:b,{name:"each",hash:{},fn:a.program(1,e,0),inverse:a.noop,data:e}))?f:"")+"
\n
\n"},useData:!0}),this.Templates.gene=f.template({1:function(a,b,c,d,e){var f,g=null!=b?b:{},h=c.helperMissing,i="function",j=a.escapeExpression;return'

\n '+j((f=null!=(f=c.name||(null!=b?b.name:b))?f:h,typeof f===i?f.call(g,{name:"name",hash:{},data:e}):f))+"\n \n chromosome "+j((f=null!=(f=c.chromosome||(null!=b?b.chromosome:b))?f:h,typeof f===i?f.call(g,{name:"chromosome",hash:{},data:e}):f))+" (start: "+j((f=null!=(f=c.start||(null!=b?b.start:b))?f:h,typeof f===i?f.call(g,{name:"start",hash:{},data:e}):f))+", end: "+j((f=null!=(f=c.end||(null!=b?b.end:b))?f:h,typeof f===i?f.call(g,{name:"end",hash:{},data:e}):f))+')\n \n

\n
\n\n \n'},3:function(a,b,c,d,e){var f;return'
\n \n
\n"},compiler:[7,">= 4.0.0"],main:function(a,b,c,d,e){var f,g=null!=b?b:{};return'
\n\n'+(null!=(f=c["if"].call(g,null!=b?b.name:b,{name:"if",hash:{},fn:a.program(1,e,0),inverse:a.noop,data:e}))?f:"")+"\n"+(null!=(f=c["if"].call(g,null!=b?b.error:b,{name:"if",hash:{},fn:a.program(3,e,0),inverse:a.noop,data:e}))?f:"")+"
\n
\n"},useData:!0}),this.Templates.index=f.template({compiler:[7,">= 4.0.0"],main:function(a,b,c,d,e){return'
\n
\n
\n

HiCBrowser is a simple web browser to visualize Hi-C and other genomic tracks. \n

It is based on HiCExplorer, a set of programs that enable you to process, normalize, analyze and visualize Hi-C data.

\n
\n
\n \n \n \n
\n
\n
\n
\n'},useData:!0}),this.Templates.loading=f.template({compiler:[7,">= 4.0.0"],main:function(a,b,c,d,e){var f;return''},useData:!0}),this.Templates.search=f.template({1:function(a,b,c,d,e){var f;return' example\n'},3:function(a,b,c,d,e){var f;return' example\n'},compiler:[7,">= 4.0.0"],main:function(a,b,c,d,e){var f,g,h=null!=b?b:{},i=c.helperMissing,j="function",k=a.escapeExpression;return'\n\n
\n\n
\n\n
\n
\n \n \n \n \n
\n\n'+(null!=(f=c["if"].call(h,null!=b?b.gene_example:b,{name:"if",hash:{},fn:a.program(1,e,0),inverse:a.noop,data:e}))?f:"")+'
\n\n
\n
\n \n \n \n \n
\n\n'+(null!=(f=c["if"].call(h,null!=b?b.browser_example:b,{name:"if",hash:{},fn:a.program(3,e,0),inverse:a.noop,data:e}))?f:"")+'
\n\n
\n
\n\n
\n \n \n \n \n \n \n \n \n \n
\n\n
\n
\n
\n\n
\n\n
\n
\n'},useData:!0}),"object"==typeof c&&c&&(b.exports=this.Templates)}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{handlebars:65}],7:[function(a,b,c){function d(a,b){b||(b=window.location.href),a=a.replace(/[\[\]]/g,"\\$&");var c=new RegExp("[?&]"+a+"(=([^&#]*)|&|#|$)","i"),d=c.exec(b);return d?d[2]?decodeURIComponent(d[2].replace(/\+/g," ")):"":null}function e(a){var b=a.target,c=b.parentNode;c.className+=c.className?" loaded":"loaded"}function f(a){var b=a.target;b.src="/static/img/not_found.png";var c=b.parentNode;c.className+=c.className?" loaded":"loaded"}function g(a,b,c){for(var d=c||0,h=0;d
").hide().append(b),$(this.el).append(h),g(document.getElementsByTagName("img"),6)}},setVisible:function(){h.show().siblings().hide(),$(this.el).css({opacity:0,visibility:"visible"}).animate({opacity:1},800)}})},{"../templates":6,underscore:82}],8:[function(a,b,c){function d(a){var b=a.toString(16);return 1==b.length?"0"+b:b}function e(a,b,c){return"#"+d(a)+d(b)+d(c)}function f(a){var b={};return b.tracks=h.compact(h.map(a.tracks,function(a,c){var d;return"boundaries"===a.file_type?(b.extent=i.extent(a.x_values),d=h.map(a.x_values,function(b,c){return{x:b,y:a.y_values[c]}}),{type:"line",name:a.section_name,className:"tads",color:"#008B8D",height:"5",data:d,interpolation:"linear"}):"bed"===a.file_type?(d=h.map(a.intervals,function(b,c){var d={x:b.bed[1],y:b.bed[2]};return"genes"===a.title&&(d.description=b.bed[3]),h.isArray(b.bed[8])&&(d.color=e.apply(null,b.bed[8])),d}),{type:"rect",name:a.title,data:d,color:"steelblue"}):void 0})),b}var g,h=a("underscore"),i=a("d3"),j=a("feature-viewer"),k=a("../templates"),l={},m=h.uniqueId("feat_viewer_");b.exports=Backbone.View.extend({initialize:function(a){this.options=a},render:function(a){if(a=h.isUndefined(a)?{}:a,a.feature_viewer=m,a.id!==l.id){$(this.el).css({opacity:0,visibility:"hidden"});var b=k.gene(a);h.isUndefined(g)||g.remove(),g=$("
").hide().append(b),$(this.el).append(g),this.renderViewer(a.tracks),$('[data-toggle="tooltip"]').tooltip()}},setVisible:function(){g.show().siblings().hide(),$(this.el).css({opacity:0,visibility:"visible"}).animate({opacity:1},800)},renderViewer:function(a){data=f(a);var b=new j(data.extent[1],"#"+m,{showAxis:!1,showSequence:!1,brushActive:!0,toolbar:!1,bubbleHelp:!1,zoomMax:10,offset:{start:data.extent[0],end:data.extent[1]}});h.each(data.tracks,b.addFeature)}})},{"../templates":6,d3:31,"feature-viewer":32,underscore:82}],9:[function(a,b,c){var d,e=a("underscore"),f=a("../templates");b.exports=Backbone.View.extend({initialize:function(a){this.options=a},render:function(a){a=e.isUndefined(a)?{}:a,$(this.el).css({opacity:0,visibility:"hidden"});var b=f.index(a);d=$("
").hide().append(b),$(this.el).empty().append(d),this.rendered=!0},rendered:!1,setVisible:function(){d.show().siblings().hide(),$(this.el).css({opacity:0,visibility:"visible"}).animate({opacity:1},800)}})},{"../templates":6,underscore:82}],10:[function(a,b,c){var d=a("underscore"),e=a("../templates"),f=d.uniqueId("loading_");b.exports=Backbone.View.extend({initialize:function(a){this.options=a},render:function(a){a=d.isUndefined(a)?{}:a,a.id=f;var b=e.loading(a);$(this.options.el).append(b)},show:function(){$("#"+f).modal({show:!0,backdrop:"static",keyboard:!1})},hide:function(){$("#"+f).modal("hide")}})},{"../templates":6,underscore:82}],11:[function(a,b,c){var d,e=a("underscore"),f=a("../templates"),g=e.uniqueId("prev_id_"),h=e.uniqueId("next_id_"),i=e.uniqueId("zoomout_id_"),j=e.uniqueId("search_input_"),k=e.uniqueId("search_input_"),l=(e.uniqueId("search_btn_"),e.uniqueId("gene_btn_")),m=e.uniqueId("browser_btn_"),n=e.uniqueId("gene_example_"),o=e.uniqueId("browser_example_"),p=!0;b.exports=Backbone.View.extend({initialize:function(a){this.options=a},events:{"click li":"onLiClick","click button":"search","keydown input":"keyAction","click a":"linkClick"},render:function(a){a=e.isUndefined(a)?{}:a.attributes,a.prev_id=g,a.next_id=h,a.zoomout_id=i,a.gene_search_input=k,a.browser_search_input=j,a.gene_btn=l,a.browser_btn=m,a.browser_example_id=o,a.gene_example_id=n;var b=f.search(a);$(this.options.el).html(b)},renderError:function(a){$("#error").html(a).show()},update:function(a){e.isUndefined(a.name)?onGeneButton():(onBrowserButton(),updateButtons(a))},search:function(){var a=p?$("#"+k).val():$("#"+j).val();if($("#error").hide(),a.length>0){var b=p?"/gene/"+a:"/browser/"+a;App.router.navigate(b,{trigger:!0})}},onLiClick:function(a){a.preventDefault();var b=$(a.currentTarget).data("id");b===l?(p=!0,this.showGeneView(),App.router.navigate("/gene",{trigger:!0,replace:!0})):b===m&&(p=!1,this.showBrowserView(),App.router.navigate("/browser",{trigger:!0,replace:!0}))},linkClick:function(a){a.preventDefault();var b=$(a.currentTarget).data("id");b===n?App.router.navigate("/gene/"+App.config.attributes.gene_example,{trigger:!0}):b===o?App.router.navigate("/browser/"+App.config.attributes.browser_example,{trigger:!0}):e.isUndefined(d)||(b===g?App.router.navigate("/browser/"+d.previous,{trigger:!0}):b===h?App.router.navigate("/browser/"+d.next,{trigger:!0}):b===i&&App.router.navigate("/browser/"+d.out,{trigger:!0}))},keyAction:function(a){13===a.which&&this.search()},showGeneView:function(a){e.isUndefined(a)||$("#"+k).val(a),$("#"+m).removeClass("active"),$("#"+l).addClass("active"),$("#"+j).parent().parent().css({opacity:0,display:"none"}),$("#"+k).parent().parent().css({opacity:0,display:"block"}).animate({opacity:1},800)},showBrowserView:function(a){d=a,e.isUndefined(a)||$("#"+j).val(a.id),$("#"+l).removeClass("active"),$("#"+m).addClass("active"),$("#"+k).parent().parent().css({opacity:0,display:"none"}),$("#"+j).parent().parent().css({opacity:0,display:"block"}).animate({opacity:1},800)}})},{"../templates":6,underscore:82}],12:[function(a,b,c){(function(c,d){"use strict";function e(b,e){function f(a){var b,c;for(b=0;a[b];b+=1)if(c=a[b],"."===c)a.splice(b,1),b-=1;else if(".."===c){if(1===b&&(".."===a[2]||".."===a[0]))break;b>0&&(a.splice(b-1,2),b-=2)}}function g(a,b){var c;return a&&"."===a.charAt(0)&&b&&(c=b.split("/"),c=c.slice(0,c.length-1),c=c.concat(a.split("/")),f(c),a=c.join("/")),a}function h(a){return function(b){return g(b,a)}}function i(a){function b(b){o[a]=b}return b.fromText=function(a,b){throw new Error("amdefine does not implement load.fromText")},b}function j(a,c,f){var g,h,i,j;if(a)h=o[a]={},i={id:a,uri:d,exports:h},g=l(e,h,i,a);else{if(p)throw new Error("amdefine with no module ID cannot be called more than once per file.");p=!0,h=b.exports,i=b,g=l(e,h,i,b.id)}c&&(c=c.map(function(a){return g(a)})),j="function"==typeof f?f.apply(i.exports,c):f,void 0!==j&&(i.exports=j,a&&(o[a]=i.exports))}function k(a,b,c){Array.isArray(a)?(c=b,b=a,a=void 0):"string"!=typeof a&&(c=a,a=b=void 0),b&&!Array.isArray(b)&&(c=b,b=void 0),b||(b=["require","exports","module"]),a?n[a]=[a,b,c]:j(a,b,c)}var l,m,n={},o={},p=!1,q=a("path");return l=function(a,b,d,e){function f(f,g){return"string"==typeof f?m(a,b,d,f,e):(f=f.map(function(c){return m(a,b,d,c,e)}),void(g&&c.nextTick(function(){g.apply(null,f)})))}return f.toUrl=function(a){return 0===a.indexOf(".")?g(a,q.dirname(d.filename)):a},f},e=e||function(){return b.require.apply(b,arguments)},m=function(a,b,c,d,e){var f,k,p=d.indexOf("!"),q=d;if(p===-1){if(d=g(d,e),"require"===d)return l(a,b,c,e);if("exports"===d)return b;if("module"===d)return c;if(o.hasOwnProperty(d))return o[d];if(n[d])return j.apply(null,n[d]),o[d];if(a)return a(q);throw new Error("No module with ID: "+d)}return f=d.substring(0,p),d=d.substring(p+1,d.length),k=m(a,b,c,f,e),d=k.normalize?k.normalize(d,h(e)):g(d,e),o[d]?o[d]:(k.load(d,l(a,b,c,e),i(d),{}),o[d])},k.require=function(a){return o[a]?o[a]:n[a]?(j.apply(null,n[a]),o[a]):void 0},k.amd={},k}b.exports=e}).call(this,a("_process"),"/node_modules/amdefine/amdefine.js")},{_process:81,path:80}],13:[function(a,b,c){!function(){function a(){return{keys:Object.keys||function(a){if("object"!=typeof a&&"function"!=typeof a||null===a)throw new TypeError("keys() called on a non-object");var b,c=[];for(b in a)a.hasOwnProperty(b)&&(c[c.length]=b);return c},uniqueId:function(a){var b=++i+"";return a?a+b:b},has:function(a,b){return g.call(a,b)},each:function(a,b,c){if(null!=a)if(f&&a.forEach===f)a.forEach(b,c);else if(a.length===+a.length)for(var d=0,e=a.length;d did not match any gene. Check the browser for examples of valid gene names as they may be an id.";App.views.search.renderError(e),d()}})}),j.on("route:getBrowser",function(){return g.isUndefined(i.browser)?(App.views.search.showBrowserView(),void d()):(App.router.navigate("/browser/"+i.browser.id,{trigger:!1}),void f(i.browser))}),j.on("route:getBrowserId",function(a){if(!g.isUndefined(i.browser)&&i.browser.id===a)return void f(i.browser);var b=new App.models.Browser({id:a}),c="Your search - "+a+" - did not match any region.";b.fetch({success:function(a){a=a.toJSON();var b=g.flatten(a.tracks);0===b.length?(App.views.search.renderError(c),d()):$.ajax({url:b[0],success:function(){i.browser=a,f(a)},error:function(){App.views.search.renderError(c),d()}})},error:function(a,b){App.views.search.renderError(c),d()}})}),j.on("route:defaultRoute",d),Backbone.history.start(),b.exports=j},{underscore:82}],6:[function(a,b,c){(function(d){var e="undefined"==typeof window?d:window,f=e.Handlebars||a("handlebars");this.Templates=this.Templates||{},this.Templates.browser=f.template({1:function(a,b,c,d,e){var f=a.lambda,g=a.escapeExpression;return'
\n \n \n
\n'},compiler:[7,">= 4.0.0"],main:function(a,b,c,d,e){var f;return'
\n
\n'+(null!=(f=c.each.call(null!=b?b:{},null!=b?b.tracks:b,{name:"each",hash:{},fn:a.program(1,e,0),inverse:a.noop,data:e}))?f:"")+"
\n
\n"},useData:!0}),this.Templates.gene=f.template({1:function(a,b,c,d,e){var f,g=null!=b?b:{},h=c.helperMissing,i="function",j=a.escapeExpression;return'

\n '+j((f=null!=(f=c.name||(null!=b?b.name:b))?f:h,typeof f===i?f.call(g,{name:"name",hash:{},data:e}):f))+"\n \n chromosome "+j((f=null!=(f=c.chromosome||(null!=b?b.chromosome:b))?f:h,typeof f===i?f.call(g,{name:"chromosome",hash:{},data:e}):f))+" (start: "+j((f=null!=(f=c.start||(null!=b?b.start:b))?f:h,typeof f===i?f.call(g,{name:"start",hash:{},data:e}):f))+", end: "+j((f=null!=(f=c.end||(null!=b?b.end:b))?f:h,typeof f===i?f.call(g,{name:"end",hash:{},data:e}):f))+')\n \n

\n
\n\n \n'},3:function(a,b,c,d,e){var f;return'
\n \n
\n"},compiler:[7,">= 4.0.0"],main:function(a,b,c,d,e){var f,g=null!=b?b:{};return'
\n\n'+(null!=(f=c["if"].call(g,null!=b?b.name:b,{name:"if",hash:{},fn:a.program(1,e,0),inverse:a.noop,data:e}))?f:"")+"\n"+(null!=(f=c["if"].call(g,null!=b?b.error:b,{name:"if",hash:{},fn:a.program(3,e,0),inverse:a.noop,data:e}))?f:"")+"
\n
\n"},useData:!0}),this.Templates.index=f.template({compiler:[7,">= 4.0.0"],main:function(a,b,c,d,e){return'
\n
\n
\n

HiCBrowser is a simple web browser to visualize Hi-C and other genomic tracks. \n

It is based on pyGenomeTracks, a program and library to plot beautiful genome browser tracks.

\n
\n
\n \n \n \n
\n
\n
\n
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start_region, end_region): self.process_bed(start_region, end_region) if chrom_region not in self.interval_tree.keys(): - chrom_region = change_chrom_names(chrom_region) + chrom_region = GenomeTrack.change_chrom_names(chrom_region) genes_overlap = self.interval_tree[chrom_region].find(start_region, end_region) diff --git a/hicbrowser/views.py b/hicbrowser/views.py index 0b15415..47db63c 100644 --- a/hicbrowser/views.py +++ b/hicbrowser/views.py @@ -1,22 +1,33 @@ import sys import numpy as np -from flask import Flask, render_template, request, send_file +from flask import Flask, render_template, request, send_file, Blueprint import os from os.path import exists import json -import hicexplorer.trackPlot -import hicbrowser.utilities +import pygenometracks.plotTracks +from pygenometracks.tracks.GenomeTrack import GenomeTrack +import pygenometracks.tracksClass as pgttc +from pygenometracks.utilities import file_to_intervaltree, opener, to_string import hicbrowser.tracks2json -from ConfigParser import SafeConfigParser +from configparser import ConfigParser -hicexplorer.trackPlot.DEFAULT_WIDTH_RATIOS = (0.89, 0.11) -hicexplorer.trackPlot.DEFAULT_MARGINS = {'left': 0.02, 'right': 0.98, 'bottom': 0, 'top': 1} +pgttc.DEFAULT_WIDTH_RATIOS = (0.01, 0.89, 0.11) +pgttc.DEFAULT_MARGINS = {'left': 0.02, 'right': 0.98, 'bottom': 0, 'top': 1} +def default(o): + """ + Transform np.integers to integers as np.integers are + not compatible with json dump + """ + if isinstance(o, np.integer): + return int(o) + else: + return o def get_TAD_for_gene(gene_name): """ @@ -29,48 +40,14 @@ def get_TAD_for_gene(gene_name): if gene_name in gene2pos: # get gene position chrom_, start_, end_ = gene2pos[gene_name] - if chrom_ not in tads_intval_tree.keys(): - if chrom_.startswith('chr'): - chrom_ = chrom_[3:] - else: - chrom_ = 'chr' + chrom_ - tad_pos = sorted( tads_intval_tree[chrom_].search(start_, end_) )[0] + if chrom_ not in tads_intval_tree: + chrom_ = GenomeTrack.change_chrom_names(chrom_) + tad_pos = sorted(tads_intval_tree[chrom_][start_:end_])[0] return chrom_, tad_pos.begin, tad_pos.end else: return None -def get_region(region_string): - """ - splits a region string into - a chrom, start_region, end_region tuple - The region_string format is chr:start-end - """ - if region_string: - # separate the chromosome name and the location using the ':' character - chrom, position = region_string.strip().split(":") - - # clean up the position - for char in ",.;|!{}()": - position = position.replace(char, '') - position_list = position.split("-") - try: - region_start = int(position_list[0]) - except IndexError: - region_start = 0 - try: - region_end = int(position_list[1]) - except IndexError: - region_end = 1e15 # a huge number - if region_start < 0: - region_start = 0 - if region_end <= region_start: - exit("Please check that the region end is larger than the region start.\n" - "Values given:\nstart: {}\nend: {}\n".format(region_start, region_end)) - - return chrom, region_start, region_end - - def snap_to_resolution(start, end): """ given a start and end, guesses the resolution and @@ -115,10 +92,10 @@ def check_static_img_folders(): try: os.makedirs(dir_path + '/images') except: - sys.exit("Images folder does not exists and can not be created.\n" - "Check that the user has permission to create the folder under\n" - "the current directory. The path for the folder is:\n" - "{}".format(dir_path + '/images/')) + raise Exception("Images folder does not exists and can not be created.\n" + "Check that the user has permission to create the folder under\n" + "the current directory. The path for the folder is:\n" + "{}".format(dir_path + '/images/')) if not os.path.isdir(dir_path + '/images/genes'): os.makedirs(dir_path + '/images/genes') @@ -132,7 +109,7 @@ def check_static_img_folders(): def main(config_file, port, numProc, template_folder=None, debug=False): - config = SafeConfigParser() + config = ConfigParser() config.readfp(open(config_file, 'r')) kwargs = {} @@ -142,7 +119,6 @@ def main(config_file, port, numProc, template_folder=None, debug=False): app = Flask(__name__, **kwargs) - from flask import Blueprint img_path = check_static_img_folders() # register an static path for images using Blueprint @@ -154,19 +130,16 @@ def main(config_file, port, numProc, template_folder=None, debug=False): # setup up the tracks. It works as follows # the config.ini file is read and split into individual tracks # that are saved on a temporary file. - # then, hicexplorer.trackPlot object is initialized with this track and + # then, pygenometracks.tracksClass.PlotTracks object is initialized with this track and # store on a list (trp_list). If the tracks were not to be splited in - # individual files, trackPlot will plot everything togeher. By splitting + # individual files, plotTracks will plot everything togeher. By splitting # them we take advantage of multiprocessing to generate each image on # a different core. Naturally, if using only one core then nothing is gained. track_file = config.get("browser", "tracks") trp_list = [] for track in track_file.split(" "): - track_list = hicbrowser.utilities.parse_tracks(track) - for temp_file_name, section_name in track_list: - print "\n{}".format(section_name) - trp_list.append(hicexplorer.trackPlot.PlotTracks(temp_file_name, fig_width=40, dpi=70)) - os.unlink(temp_file_name) + trp_list.append(pgttc.PlotTracks(track)) + tad_img_root = img_path + '/genes' img_root = img_path + '/browser' @@ -176,7 +149,7 @@ def main(config_file, port, numProc, template_folder=None, debug=False): tads_file = config.get('general', 'TAD intervals') global tads_intval_tree - tads_intval_tree, __, __ = hicexplorer.trackPlot.file_to_intervaltree(tads_file) + tads_intval_tree, __, __ = file_to_intervaltree(tads_file) # initialize gene name to position mapping genes = config.get('general', 'genes') @@ -188,9 +161,9 @@ def main(config_file, port, numProc, template_folder=None, debug=False): track_file = config.get('general', 'tracks') tads = hicbrowser.tracks2json.SetTracks(track_file, fig_width=40) - from hicexplorer.trackPlot import opener with opener(genes) as fh: for line in fh.readlines(): + line = to_string(line) if line.startswith('browser') or line.startswith('track') or line.startswith('#'): continue gene_chrom, gene_start, gene_end, gene_name = line.strip().split("\t")[0:4] @@ -201,7 +174,7 @@ def main(config_file, port, numProc, template_folder=None, debug=False): sys.stderr.write("Problem with line {}".format(line)) pass gene2pos[gene_name.lower()] = (gene_chrom, gene_start, gene_end) - + @app.route('/', methods=['GET']) def index(): return render_template("index.html") @@ -238,7 +211,6 @@ def get_tad(gene_name): data['tracks'] = d res = json.dumps(data) - return res @app.route('/browser/', methods=['GET']) @@ -248,10 +220,11 @@ def browser(query): # check if the query is a valid gene name if gene_name in gene2pos: chromosome, start, end = gene2pos[gene_name] - start -= 50000 + start -= 50000 if start > 50000 else 0 end += 50000 else: - chromosome, start, end = get_region(query.strip()) + chromosome, start, end = pygenometracks.plotTracks.get_region(query.strip()) + print("chr:{}".format(chromosome)) if end - start < 10000: sys.stderr.write("region to small ({}bp), enlarging it.".format(end - start)) start -= 5000 @@ -340,7 +313,7 @@ def browser(query): 'content': content, 'start': start, 'end': end} - json_data = json.dumps(data) + json_data = json.dumps(data, default=default) return json_data @@ -355,7 +328,7 @@ def get_image(): return None if query: query = query.strip() - chromosome, start, end = get_region(query) + chromosome, start, end = pygenometracks.plotTracks.get_region(query) outfile = "{}/{}_{}_{}_{}.png".format(img_root, chromosome, @@ -364,7 +337,7 @@ def get_image(): img_id) # if the figure does no exists, then # hicexplorer.trackPlot is called (trp_list[img_id] contains - # an instance of hicexplorer.trackPlot + # an instance of pygenometracks.tracksClass.PlotTracks) if not exists(outfile): trp_list[img_id].plot(outfile, chromosome, start, end) diff --git a/setup.py b/setup.py index e00b37f..ebb9644 100755 --- a/setup.py +++ b/setup.py @@ -19,24 +19,24 @@ def update_version_py(): if not os.path.isdir(".git"): - print "This does not appear to be a Git repository." + print("This does not appear to be a Git repository.") return try: p = subprocess.Popen(["git", "describe", "--tags", "--always"], stdout=subprocess.PIPE) except EnvironmentError: - print "unable to run git, leaving hicbrowser/_version.py alone" + print("unable to run git, leaving hicbrowser/_version.py alone") return stdout = p.communicate()[0] if p.returncode != 0: - print "unable to run git, leaving hicbrowser/_version.py alone" + print("unable to run git, leaving hicbrowser/_version.py alone") return ver = stdout.strip() f = open("hicbrowser/_version.py", "w") f.write(VERSION_PY % ver) f.close() - print "set hicbrowser/_version.py to '%s'" % ver + print("set hicbrowser/_version.py to '%s'" % ver) def get_version(): @@ -73,7 +73,7 @@ def run(self): long_description=open('README.md').read(), install_requires=[ "flask", - "hicexplorer", + "pygenometracks>=3", "bx-python" ], cmdclass={'sdist': sdist}