def __init__(self, fileName,rawFileName=None):
self.molecules, self.rules, _ = readBNGXML.parseXML(fileName)
self.dependencies, self.patternXreactions, _, _ = componentGroups.getContextRequirements(fileName, collapse=False)
self.transposePatternsReactions()
self.reverseDependencies = componentGroups.reverseContextDict(self.dependencies)
self.moleculeMotifDict, self.motifMoleculeDict = self.classifyPairsByMotif(self.reverseDependencies)
if rawFileName:
self.processRawSBML(rawFileName)
else:
self.rawRules = {}
def __init__(self, fileName, rawFileName=None):
self.molecules, self.rules, _ = readBNGXML.parseXML(fileName)
self.dependencies, self.patternXreactions, _, _ = componentGroups.getContextRequirements(
fileName, collapse=False)
self.transposePatternsReactions()
self.reverseDependencies = componentGroups.reverseContextDict(
self.dependencies)
self.moleculeMotifDict, self.motifMoleculeDict = self.classifyPairsByMotif(
self.reverseDependencies)
if rawFileName:
self.processRawSBML(rawFileName)
else:
self.rawRules = {}
def defineConsole():
"""
defines the program console line commands
"""
parser = argparse.ArgumentParser(description="SBML to BNGL translator")
parser.add_argument("-f1",
"--file1",
type=str,
help="reference file",
required=True)
parser.add_argument("-f2",
"--file2",
type=str,
help="comparison file",
required=True)
# parser.add_argument('-o', '--output', type=str, help='output file', required=True)
return parser
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
context1 = componentGroups.getContextRequirements(namespace.file1, False)
context2 = componentGroups.getContextRequirements(namespace.file2, False)
result = compareModelsContext(namespace.file1, namespace.file2, context1,
context2)
import pprint
print(pprint.pprint(result))
moleculeNameIntersection, componentNameIntersection = modelComparison.compareModelsStructurally(fileName1, fileName2, moleculemapping, componentmapping)
differences, simCounter, totCounter = modelComparison.obtainContextDifferences(fileName1, fileName2, moleculeNameIntersection, componentNameIntersection,context1,context2)
#evaluateDifferences(differences, fileName1, fileName2, fileName1raw, fileName2raw)
#with open(outputle, 'w') as f:
# f.write(yaml.dump(differences))
return fileName1, fileName2, simCounter, totCounter, differences
def defineConsole():
"""
defines the program console line commands
"""
parser = argparse.ArgumentParser(description='SBML to BNGL translator')
parser.add_argument('-f1', '--file1', type=str, help='reference file', required=True)
parser.add_argument('-f2', '--file2', type=str, help='comparison file', required=True)
#parser.add_argument('-o', '--output', type=str, help='output file', required=True)
return parser
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
context1= componentGroups.getContextRequirements(namespace.file1,False)
context2 = componentGroups.getContextRequirements(namespace.file2,False)
result = compareModelsContext(namespace.file1, namespace.file2, context1,context2)
import pprint
print pprint.pprint(result)
#print len(result[0])
