def readrpSBMLtar(inputTar):
rpsbml_paths = {}
with tarfile.open(inputTar) as tar:
for member in tar.getmembers():
rpsbml_paths[member.name] = rpRanker.rpSBML(
member.name,
libsbml.readSBMLFromString(
tar.extractfile(member).read().decode("utf-8")))
return rpsbml_paths
return rpsbml_paths
if __name__ == "__main__":
parser = argparse.ArgumentParser(
'Given an SBML model and the generated SBML heterologous pathway by RetroPath2.0, merge the two'
)
parser.add_argument('-inModel', type=str)
parser.add_argument('-inSBMLtar', type=str)
parser.add_argument('-outSBMLtar', type=str)
params = parser.parse_args()
#sbml read the different mode
rpsbml_paths = readrpSBMLtar(params.inSBMLtar)
for rpsbml_name in rpsbml_paths:
#read the input sbml model
input_rpsbml = rpRanker.rpSBML('inputMergeModel')
input_rpsbml.readSBML(params.inModel)
rpsbml_paths[rpsbml_name].mergeModels(input_rpsbml.model)
rpfba = rpRanker.rpFBA(input_rpsbml)
rpfba.allObj()
##### pass FBA results to the original model ####
groups = rpfba.rpsbml.model.getPlugin('groups')
rp_pathway = groups.getGroup('rp_pathway')
for member in rp_pathway.getListOfMembers():
reacFBA = rpfba.rpsbml.model.getReaction(member.getIdRef())
reacIN = rpsbml_paths[rpsbml_name].model.getReaction(
member.getIdRef())
reacIN.setAnnotation(reacFBA.getAnnotation())
#rpsbml_paths[rpsbml_name] = rpsbml_paths[rpsbml_name]
input_rpsbml = None
writerpSBMLtar(rpsbml_paths, params.outSBMLtar)
#!/usr/bin/env python3
import argparse
import sys
sys.path.insert(0, '/home/')
import rpRanker
if __name__ == "__main__":
parser = argparse.ArgumentParser(
'Generate the sink from a model SBML by specifying the compartment')
parser.add_argument('-inSBML', type=str)
parser.add_argument('-outSink', type=str)
parser.add_argument('-compartmentId', type=str, default='MNXC3')
#TODO: check that the compartmentId exists and return an error if not. Idea: print the list of available compartments if error is found
params = parser.parse_args()
rpsbml = rpRanker.rpSBML('tmp')
rpsbml.readSBML(params.inSBML)
rpreader = rpRanker.rpReader()
rpreader.genSink(rpsbml, params.outSink, params.compartmentId)
exit(0)