addingEvidenceCodes_1.py

Adds controlled vocabulary terms to a reaction in a model.

#!/usr/bin/env python
##
## \file    addingEvidenceCodes_1.py
## \brief   adds controlled vocabulary terms to a reaction in a model
## \author  Sarah Keating
##
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import sys
import os.path
from libsbml import *

def main (args):
  """usage: addingEvidenceCodes_1 <input-filename> <output-filename>
     Adds controlled vocabulary term to a reaction
  """
  if len(args) != 3:
    print(main.__doc__)
    sys.exit(2)

  d = readSBML(args[1])
  errors = d.getNumErrors()

  if errors > 0:
    print("Read Error(s):\n")
    d.printErrors()

    print("Correct the above and re-run.\n")
  else:
    n = d.getModel().getNumReactions()

    if n <= 0:
        print("Model has no reactions.\n Cannot add CV terms\n")
    else:
        r = d.getModel().getReaction(0)

        # check that the reaction has a metaid
        # no CVTerms will be added if there is no metaid to reference
        # 
        if not r.isSetMetaId():
            r.setMetaId("metaid_0000052")

        cv1 = CVTerm(BIOLOGICAL_QUALIFIER)
        cv1.setBiologicalQualifierType(BQB_IS_DESCRIBED_BY)
        cv1.addResource("urn:miriam:obo.eco:ECO%3A0000183")

        r.addCVTerm(cv1)

        cv2 = CVTerm(BIOLOGICAL_QUALIFIER)
        cv2.setBiologicalQualifierType(BQB_IS)
        cv2.addResource("urn:miriam:kegg.reaction:R00756")
        cv2.addResource("urn:miriam:reactome:REACT_736")

        r.addCVTerm(cv2)

        writeSBML(d, args[2])
  return errors


if __name__ == '__main__':
  main(sys.argv)