brsynth/rpextractsink repository overview

⁠rpExtractSink

• Docker image: brsynth/rpextractsink-standalone⁠

Tool that takes for input an SBML file and uses the MIRIAM annotations of the chemical species within a given compartment to find their InChI structures. Performs FVA to remove dead end metabolites. The output is a CSV RetroPath2.0 friendly CSV file that can be used as sink input.

⁠Input

Required:

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

Addtional information:

• -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_sink: (string) Path to the output csv file

⁠Dependencies

• Base docker image: brsynth/rpbase⁠
• Cache docker image: brsynth/rpcache⁠

⁠Installing

To compile the docker use the following command:

docker build -t brsynth/rpextractsink-standalone .

⁠Running the test

To run the test, run the following command:

python run.py -input_sbml test/e_coli_model.sbml -output_sink test/test_rpExtractSink.csv

⁠Contributing

Please read CONTRIBUTING.md⁠ for details on our code of conduct, and the process for submitting pull requests to us.

⁠Versioning

v0.1

⁠Authors

• Melchior du Lac
• Thomas Duigou

⁠License

MIT⁠

⁠Acknowledgments

• Joan Hérisson

⁠How to cite rpMakeSource?