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])