Prolipipe : large-scale assessment of metabolic profiles on bacteria focusing on specific pathways.

Workflow to reconstruct multiple metabolic graphs and assess capacity to synthesize specific compounds.

Table of contents

• License
• Installation
  • Dependencies
  • pip
• Usage

License

This workflow is licensed under the GNU GPL-3.0-or-later, see the LICENSE file for details.

Installation

Dependencies

Prolipipe relies on "MeReco" package

These python packages are needed :

• padmet
• pandas

pip

If you have installed all the dependencies listed here and on MeReco's page, you can just install prolipipe with:

pip install mereco
pip install prolipipe

Usage

prolipipe.py [-h] -i INPUT -o OUTPUT --tax TAXFILE --padmet_ref PATH_TO_PADMET_REF --ptsc PTSC --ptsi PTSI --pwy PWY_FOLD --strain STRAIN
                                    [--annot ANNOT] [--egg_path EGG_PATH] [--bak_path BAK_PATH] [-c CPUS] [-a] [-k] [-q]