rpExtractSink

RetroPath2 sink generator. From a given SBML file, the tool will extract all the sink molecules and generate a csv file with the InChI structures. For each molecule, the InChI will be get from:

1. The local cache (rrCache), if available
2. The MetaNetX database from MIRIAM URLs (MetaNetX first)

Input

Required:

• input_sbml: (string) Path to the input SBML file

Optional:

• --remove-dead-end: (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites
• --compartment-id: (string, default: 'c') Specify the compartment from which to extract the sink molecules. The default are for MetaNetX files
• --standalone: (boolean, default: False) If True, do not retrieve InChI from Internet
• --cache-dir: (string, default: None) Path to the cache directory

Output

• output_sbml: (string) Path to the output csv file

Install

conda install -c conda-forge rpextractsink

Use

Function call from Python code

from rr_cache import rrCache
from rpextractsink import genSink

cache = rrCache(
    attrs=['cid_strc'],
    cache_dir=args.cache_dir,
    logger=logger
)
sink = genSink(
    cache,
    args.input_sbml
)

Run from CLI

python -m rpextractsink --help

Tests

Test can be run with the following commands:

Natively

python -m pytest

Authors

• Joan Hérisson
• Thomas Duigou, Melchior du Lac

License

This project is licensed under the MIT License - see the LICENSE file for details