# -*- coding: utf-8 -*-
"""
Description:
compare reactions in sbml and padmet file
::
usage:
compare_sbml_padmet.py --padmet=FILE --sbml=FILE
option:
-h --help Show help.
--padmet=FILE path of the padmet file
--sbml=FILE path of the sbml file
"""
from padmet.classes import PadmetSpec
import padmet.utils.sbmlPlugin as sp
import libsbml
import docopt
[docs]def main():
args = docopt.docopt(__doc__)
sbml_file = args["--sbml"]
reader = libsbml.SBMLReader()
sbml_document = reader.readSBML(sbml_file)
for i in range(sbml_document.getNumErrors()):
print(sbml_document.getError(i).getMessage())
padmet = PadmetSpec(args["--padmet"])
compare_sbml_padmet(sbml_document, padmet)
[docs]def compare_sbml_padmet(sbml_document, padmet):
"""
compare reactions ids in sbml vs padmet, return nb of reactions in both
and reactions id not in sbml or not in padmet
Parameters
----------
padmet: padmet.classes.PadmetSpec
padmet to udpate
sbml_file: libsbml.document
sbml document
"""
sbml_model = sbml_document.getModel()
sbml_listOfReactions = set([sp.convert_from_coded_id(r.getId())[0] for r in sbml_model.getListOfReactions()])
padmet_reaction = set([node.id for node in padmet.dicOfNode.values() if node.type == "reaction"])
diff = sbml_listOfReactions.difference(padmet_reaction)
diff_inv = padmet_reaction.difference(sbml_listOfReactions)
print("%s reaction in sbml" %len(sbml_listOfReactions))
print("%s reaction in padmet" %len(padmet_reaction))
print("%s reaction in sbml not in padmet" %len(diff))
for i in diff:
print("\t%s" %i)
print("%s reaction in padmet not in sbml" %len(diff_inv))
for i in diff_inv:
print("\t%s" %i)
if __name__ == "__main__":
main()