def getContext(fileName, auxDirectory=None):
if auxDirectory:
auxFile = fileName.split('/')[-1]
with open(os.path.join(auxDirectory, '{0}.dump'.format(auxFile))) as f:
context = pickle.load(f)
stateDict = pickle.load(f)
else:
context, stateDict = componentGroups.getContextRequirements(fileName)
return [context, stateDict]
def getContext(fileName, auxDirectory=None):
if auxDirectory:
auxFile = fileName.split("/")[-1]
with open(os.path.join(auxDirectory, "{0}.dump".format(auxFile))) as f:
context = pickle.load(f)
stateDict = pickle.load(f)
else:
context, stateDict = componentGroups.getContextRequirements(fileName)
return [context, stateDict]
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 createContextInformation(inputDirectory,outputDirectory):
bngxml = getFiles(inputDirectory, 'xml')
progress = progressbar.ProgressBar()
fullContextDict = {}
for idx in progress(range(len(bngxml))):
fileName = bngxml[idx]
#molecules,rules,_ = parseXML(fileName)
extendedInformation, backup = componentGroups.getContextRequirements(fileName,False)
fullContextDict[fileName] = extendedInformation
with open(os.path.join(outputDirectory, '{0}.dump'.format(fileName.split('/')[-1])), 'w') as f:
pickle.dump(default_to_regular(extendedInformation), f)
pickle.dump(default_to_regular(backup), f)
#collapsedContactMap.createCollapsedContact(rules,molecules,[1],fileName + '.gml',extendedInformation )
with open(os.path.join(outputDirectory, '{0}.dump'.format(inputDirectory), 'w')) as f:
molecules, rules, _ = parseXML(fileName)
graph, graphDictionary = createCollapsedContact(rules, molecules, [1], outputfilename, extendedInformation,
contextOnlyFlag, nullContextFlag, separateGraphsFlag, motifFlag, bipartiteFlag)
if separateGraphsFlag:
for graphObject in graphDictionary:
nx.write_gml(graphDictionary[graphObject], '{0}_{1}.gml'.format(fileName.split('.')[0], graphObject))
else:
nx.write_gml(graph, outputfilename)
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
inputFile = namespace.input
if namespace.output is not None:
outputFile = namespace.output
else:
outputFile = inputFile + '.gml'
collapseFlag = False if namespace.expand else True
if namespace.rulify:
extendedInformation, _, exclusionCliques, processNodes = componentGroups.getContextRequirements(inputFile, collapse=collapseFlag,
motifFlag=namespace.motifs, excludeReverse=True)
else:
extendedInformation = {}
extendedInformationDict = {'extendedInformation': extendedInformation,
'exclusionCliques': exclusionCliques, 'processNodes': processNodes}
main(inputFile, outputFile, extendedInformationDict, namespace.context_only, namespace.null_context,
namespace.separate_graphs, namespace.motifs, namespace.bipartite)
#addAnnotations('fceri_ji')
def defineConsole():
parser = argparse.ArgumentParser(description='SBML to BNGL translator')
parser.add_argument('-i', '--input', type=str, help='settings file',required=True)
parser.add_argument('-o', '--output', type=str, help='output directory')
parser.add_argument('-r', '--rulify', action='store_true')
return parser
def main(fileName,outputfilename,extendedInformation):
molecules,rules,_ = parseXML(fileName)
createCollapsedContact(rules,molecules,[1],outputfilename,extendedInformation)
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
inputFile = namespace.input
if namespace.output != None:
outputFile = namespace.output
else:
outputFile = inputFile + '.gml'
if namespace.rulify:
extendedInformation = componentGroups.getContextRequirements(inputFile)
else:
extendedInformation = {}
main(inputFile,outputFile,extendedInformation)
#addAnnotations('fceri_ji')
else:
nx.write_gml(graph, outputfilename)
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
inputFile = namespace.input
if namespace.output is not None:
outputFile = namespace.output
else:
outputFile = inputFile + '.gml'
collapseFlag = False if namespace.expand else True
if namespace.rulify:
extendedInformation, _, exclusionCliques, processNodes = componentGroups.getContextRequirements(
inputFile,
collapse=collapseFlag,
motifFlag=namespace.motifs,
excludeReverse=True)
else:
extendedInformation = {}
extendedInformationDict = {
'extendedInformation': extendedInformation,
'exclusionCliques': exclusionCliques,
'processNodes': processNodes
}
main(inputFile, outputFile, extendedInformationDict,
namespace.context_only, namespace.null_context,
namespace.separate_graphs, namespace.motifs, namespace.bipartite)
#addAnnotations('fceri_ji')
