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.inference.pathologic.pythonic \
    --reactome reaction.list \
    --output pathway.list \
    --taxon 561 \
    --reason pan2met.log

The pan2met.inference.pathologic.pythonic module command line interface requires the following options:

• --reactome -- a file with a list of reaction identifiers
• --output -- output file with the list of predicted pathways
• --taxon -- an integer corresponding to the taxonomy identifier from the NCBI Taxonomy
• --reason -- a file to log a reason leading to keep the pathway or to reject it

Installation

From source

1. Clone this repository

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

2. Install locally in a virtual environment

   python3 -m venv .venv/pan2met
   source .venv/pan2met/bin/activate
   pip install -e .

Setup

Create a configuration file, in e.g. conf/configuration.ini, from provided example configuration file:

[reactome]

[inference]
pathway_score_threshold = 0.35

[reference]
ncbi_taxonomy = /mnt/shared/bank/NCBI-Taxonomy/taxdmp_2026-01-01
source = metabiantes

[metabiantes]
database = metabiantes

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 source 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 metabiantes git repository for instructions on how to setup a metabiantes SQL database.

Download support materials

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.