rpextractsink

RetroPath2 sink generator

Input

Required:

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

Optional:

• --remove_dead_end: (boolean, default: True) Perform FVA evaluation to remove dead end metabolites
• --compartment_id: (string, default: MNXC3) Specify the compartment from which to extract the sink molecules. The default are for MetaNetX files

Output

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

Install

From pip

[sudo] python -m pip install rpextractsink

From Conda

[sudo] conda install -c brsynth -c conda-forge -c bioconda rpextractsink

Use

Function call from Python code

from rpextractsink import rpextractsink

sink = rpExtractSink(input_sbml, output_sink)
sink.genSink()

If parameters from CLI have to be parsed, the function build_args_parser is available:

from rpextractsink import build_args_parser

parser = buildparser()
params = parser.parse_args()

Run from CLI

python -m rpextractsink <input_sbml> <output_sink> [--compartment_id COMPARTMENT_ID] [--remove_dead_end REMOVE_DEAD_END]

Tests

Test can be run with the following commands:

Natively

cd tests
pytest -v

CI/CD

For further tests and development tools, a CI toolkit is provided in ci folder (see ci/README.md).

Authors

• Melchior du Lac
• Thomas Duigou, Joan Hérisson

License

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