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rplibs

Libraries for rpTools, contains:

  • rpSBML
  • inchikeyMIRIAM

rpSBML

Defines SBML structure with additional fields relative to RetroPath2 objects.

Install

Please see rptool documentation.

Test

Please follow instructions below ti run tests:

cd tests
pytest -v

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

Merging

rpSBML class allows the merging between txo rpSBML objects. We use this method to merge an heterologue pathway and a model.

Compartments

The compartment of the pathway to each compartment of the model. The comparison is done by ID, name or MIRIAM annotations. If a model compartment matches, then we rename the compartment of each species of the pathway to the name of the model matched compartment. Otherwise, the pathway compartment is added to the model.

inchikeyMIRIAM

Uses the rrCache to parse an SBML file to find all the chemical species, and try to recover the inchikey and add it to the MIRIAM annotation.

Statisticis

To print statistics on pathways, type:

python -m rptools.rplibs.stats --pathways <Pathway_1> <Pathway_2>

Authors

  • Melchior du Lac
  • Joan Hérisson

Acknowledgments

  • Thomas Duigou

Licence

brs_libs is released under the MIT licence. See the LICENCE file for details.