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rpScore

Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.

Input

Positional argument:

  • infile: (string) Path to pathway (rpSBML) file
  • outfile: (string, required if one single input file is passed) path to store the scored pathway

Optional arguments:

  • --no_of_rxns_thres: (int, default=10) number of reactions above which a pathway is not scored (too long)
  • --data_train_file: (string) path to the trained data
  • --log: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical'
  • --version: Display program's version and exit

Install

Please see rptool documentation.

Run

From Python code

from rptools.rpscore import predict_score
from rptools.rplibs import rpPathway

pathway = rpPathway(
    infile='tests/rpscore/data/pathway.xml'
)

global_score = predict_score(pathway)

From CLI

python -m rptools.rpscore <input_rpsbml> <output_rpsbml>

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

  • Jean-Loup Faulon
  • Joan Hérisson

License

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

Acknowledgments

  • Thomas Duigou