/rpReader

Convert the results of RetroPath2 to SBML files

Primary LanguagePython

rpReader docker

RetroPath2.0 and rp2paths to SBML conversion tool. Takes for input the output of both RetroPath2.0 and rp2paths or RetroPath3.0 and generates a series of enriches SBML files with all the files contained within them.

Input

Required:

  • -rp2paths_pathways: (string) Path to the rp2paths pathways file
  • -rp2paths_compounds: (string) Path to the rp2paths compounds file
  • -rp2_pathways: (string) Path to the RetroPath2.0 pathways file

Advanced options:

  • -upper_flux_bound: (integer, default=9999) Upper flux bound value
  • -lower_flux_bound: (integer, default=0) Lower flux bound value
  • -maxRuleIds: (integer, default=2) Number of subpaths per paths
  • -pathway_id: (string, default=rp_pathway) ID of the heterologous pathway
  • -compartment_id: (string, default=MNXC3 (i.e. cytoplasm)) Heterologous pathway compartment ID
  • -species_group_id: (string, default=central_species) ID of the central species, i.e. not cofactors, in the heterologous reactions

Output

  • -outputTar: (string) Path to the output tar.xz file

Dependencies

Building the docker

To build the docker locally, run the following command in the root folder of the project:

docker build -t brsynth/rpreader-standalone -f Dockerfile .

Running the test

To test untar the test.tar.xz file and run the following command:

Locally

python tool_rp2Reader.py -rp2paths_compounds test/rp2paths_compounds.csv -rp2_pathways test/rp2_pathways.csv -rp2paths_pathways test/rp2paths_pathways.csv -output test/test_rpReader.tar

Docker

python run_rp2.py -rp2paths_compounds test/rp2paths_compounds.csv -rp2_pathways test/rp2_pathways.csv -rp2paths_pathways test/rp2paths_pathways.csv -output test/test_rpReader.tar

Dependencies

Contributing

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

Version

v0.1

Authors

  • Melchior du Lac

License

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

Acknowledgments

  • Thomas Duigou
  • Joan Hérisson

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