Quickstart

Warning

We assume that you arrive at this step having installed the tool first (see Installation), for instance in a Python virtual environment, or conda (mamba) environment.

The following quickstart guide will help you get started with MetaNetMap. Code examples are provided for each step, applying to toy data included in the repository.

Two modes are available for testing, with an option to enable or disable partial match.

The Partial match is optional, as it can be time-consuming. It is a post-processing step applied to metabolites or IDs that were not successfully mapped during the initial run. These unmatched entries are re-evaluated using specific strategies, which increase the chances of finding a match (e.g., via ChEBI, InChIKey, or enantiomer simplification).

Tests use a dedicated third-party conversion table relying on MetaCyc data. Because licence restrictions apply, we provide the possibility to create such a table using freely available MetaNetX data. This conversion datatable can be created easily using the folowing command:

metanetmap build_db --db metanetx

Classic mode

The classic mode allows you to input a single metabolomic annotation profile (tabulated file, .maf or .tsv) or a directory containing multiple metabolomic annotation profiles, and a unique metabolic network (.sbml or .xml) to which metabolites will be mapped.

metanetmap test

Classic mode with partial match activated:

metanetmap test --partial_match

Community mode

The “community” mode allows you to input a directory containing multiple metabolomic annotation profiles (tabulated files, .maf or .tsv), as well as a directory containing multiple metabolic networks (.sbml or .xml).

metanetmap test --community

Community mode with partial match activated:

metanetmap test --community --partial_match

For more details on modes refer to Usage.