pan2met

A python library / CLI to predict metabolic networks at the pangenome scale.

Usage

To predict metabolic pathways with pan2met, you will need a set of catalyzed reactions. To identify such a set of reactions, you can use the nextflow workflow pan2met-wf. This workflow supports multiple enzyme annotation sources to map proteins to MetaCyc reactions.

Given a file reaction.list with a list of MetaCyc reaction identifiers, you can use the following command to predict pathways using a set of decision rules.

python3 -m pan2met metabolism \
    --reactions reaction.list \
    --output pathway.list \
    --taxon-id 561 \
    --reason pan2met.log

usage: pan2met metabolism [-h] -r REACTIONS -o OUTPUT [--reason REASON] [-t TAXON_ID]

infer the (pan)metabolism (i.e., a set of expected metabolic pathways)

options:
  -h, --help            show this help message and exit
  -r, --reactions REACTIONS
                        a file listing the reactions found in the (pan)-reactome
  -o, --output OUTPUT   the path of the output file listing all identifiers of pathway infered to be present
  --reason REASON       the path to an output file with a reason log.
  -t, --taxon-id TAXON_ID
                        the NCBI-Taxonomy tax id of the target organism.

For more information on how to use pan2met, please refer to the pan2met documentation

Installation

From source

1. Clone this repository

   git clone https://github.com/labgem/pan2met.git
   cd pan2met
   

2. Install locally in a pixi virtual environment

   pan2met uses graph-tool to manage the pangenome graph datastructure. As graph-tool is not available on PyPI.org, being a C++ backed Python package, you will need to install graph-tool on your own with your OS package management system, or using the conda-forge distribution. For an easy environment creation, you can use pixi:

   pixi shell
   

   pip install .
   

   Then, the pan2met command line interface should be installed and available in your PATH:

   pan2met --version
   

Setup

Create a configuration file, in e.g. configuration.yaml, from provided example configuration file. You can consult the configuration yaml schema the configuration must stick to.

You will most probably need to adapt the reference section.

1. Update ncbi_taxonomy directory path, with the path to the directory with a dump of the NCBI-Taxonomy.
2. Update the knowledge_base key, to either metabiantes or padmet depending of the format of metabolism knowledge base to use.

If you use metabiantes as the reference knowledge base for metabolism, please refer to the metabiantes git repository for instructions on how to setup a metabiantes SQL database.

Download the reference material

Reference taxonomy from the NCBI Taxonomy database

Download a NCBI Taxonomy dump from https://ftp.ncbi.nih.gov/pub/taxonomy/ to a local folder, and adapt the path in the configuration file in section [reference], key ncbi_taxonomy.