pan2met

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

Installation

From source

1. Clone this repository

   git clone https://gitlab.com/sortion/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_cutoff = 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 directory where lies the NCBI-Taxonomy dump.
2. Update the source key, to either metabiantes or padmet depending of the source of metabolism knowledge.

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.

Fix clyngor clingo Answer set parsing error

On clingo v5.8.0 (at least), the output Answer set is followed by the execution time, e.g.:

Answer 1 (Time: 0.608s)

This cause an int parse error in clyngor (see clyngor merged pr #34), until a new version is available on PyPI including this fix, if you have a clingo version having the execution time in answer set output, you should install clyngor with:

pip install git+https://github.com/Aluriak/clyngor@master