addCVTerms.py

Adds controlled vocabulary terms to a species in a model.

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

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

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

  if errors > 0:
      print("Read Error(s):")
      d.printErrors()
      print("Correct the above and re-run.")
  else:
      n = d.getModel().getNumSpecies()

      if n <= 0:
          print("Model has no species.\n Cannot add CV terms\n")
      else:
          s = d.getModel().getSpecies(0)

          if not s.isSetMetaId(): 
            s.setMetaId('unique_id_1')
  
          cv = CVTerm()
          cv.setQualifierType(BIOLOGICAL_QUALIFIER)
          cv.setBiologicalQualifierType(BQB_IS_VERSION_OF)
          cv.addResource("http://www.geneontology.org/#GO:0005892")

          cv2 = CVTerm()
          cv2.setQualifierType(BIOLOGICAL_QUALIFIER)
          cv2.setBiologicalQualifierType(BQB_IS)
          cv2.addResource("http://www.geneontology.org/#GO:0005895")

          cv1 =  CVTerm()
          cv1.setQualifierType(BIOLOGICAL_QUALIFIER)
          cv1.setBiologicalQualifierType(BQB_IS_VERSION_OF)
          cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394")

          s.addCVTerm(cv)
          s.addCVTerm(cv2)
          s.addCVTerm(cv1)

          writeSBML(d, args[2])

  return errors


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