def parse( self, rxnfile, metabolitefile, fluxlimitfile, objectivefile, analysisName, exchangeFile = None):
#networkParser = MetabolicNetworkFlatFileParser()
network = self.networkParser.parse( rxnfile, metabolitefile )
fluxModel = FluxModel( network )
if fluxlimitfile != '' and fluxlimitfile != None:
fluxLimits= self.fluxLimitParser.parse( fluxlimitfile )
else:
fluxLimits = FluxLimit()
if objectivefile != '' and objectivefile != None:
objective= self.objectiveParser.parse( objectivefile )
else:
objective = Objective()
if exchangeFile != '' and exchangeFile != None:
( reactions, objective, limit ) = self.exchangeParser.parse(exchangeFile)
network.addReactionMap(reactions)
fluxLimits.extend(limit)
if self.directionCheck:
fluxLimits = self.checkDirectionality(network, fluxLimits)
fluxModel.addAnalysis( analysisName, objective, fluxLimits )
return fluxModel
def parseGenConfig(self,config,modelName):
dir = config["basedir"]
network = None
fluxLimits = None
smmData = None
objective = None
metaboliteData = None
if config["rxnfile"] != '':
rxnFile =dir + config["rxnfile"]
network = self.networkParser.parse(rxnFile)
else:
network = MetabolicNetwork('')
if config["smmfile"] != '':
smmFile = dir + config["smmfile"]
metaboliteData = self.smmParser.parse(smmFile)
if config["fluxlimitfile"] != '':
fluxLimitFile = dir + config["fluxlimitfile"]
fluxLimits = self.fluxLimitParser.parse(fluxLimitFile)
else:
fluxLimits = FluxLimit()
if config["objectivefile"] != '':
objectiveFile = dir + config["objectivefile"]
objective = self.objectiveParser.parse(objectiveFile)
else:
objective = Objective()
if config["exchangefile"] != '':
exchangeFile = dir + config["exchangefile"]
( reactions, objective, limit ) = self.exchangeParser.parse(exchangeFile)
network.addReactionMap(reactions)
fluxLimits.extend(limit)
if self.directionCheck:
fluxLimits = self.checkDirectionality(network, fluxLimits)
#Add data to collector
if network != None:
result = FluxModel(network)
if metaboliteData != None:
result.setMetaboliteData(metaboliteData)
if objective != None and fluxLimits != None:
result.addAnalysis( modelName, objective, fluxLimits )
return result
def generateModel(self,modelName=None):
if modelName == None:
modelName = self.modelName
dir = self.basedir
network = None
fluxLimits = None
objective = None
metaboliteData = None
if self.rxnfile != '':
rxnFile =dir + self.rxnfile
network = self.networkParser.parse(rxnFile)
else:
network = MetabolicNetwork('')
if self.smmfile != '':
smmFile = dir + self.smmfile
metaboliteData = self.smmParser.parse(smmFile)
if self.fluxlimitfile != '':
fluxLimitFile = dir + self.fluxlimitfile
fluxLimits = self.fluxLimitParser.parse(fluxLimitFile)
else:
fluxLimits = FluxLimit()
if self.objectivefile != '':
objectiveFile = dir + self.objectivefile
objective = self.objectiveParser.parse(objectiveFile)
else:
objective = Objective()
if self.directionCheck:
fluxLimits = self.checkDirectionality(network, fluxLimits)
#Add data to collector
if network != None:
result = FluxModel(network)
if metaboliteData != None:
result.setMetaboliteData(metaboliteData)
if objective != None and fluxLimits != None:
result.addAnalysis( modelName, objective, fluxLimits )
return result
def parseMultipleAnalysis( self, rxnfile, metabolitefile, fluxlimitfiles, objectivefiles, analysisNames ):
networkParser = MetabolicNetworkFlatFileParser()
network = networkParser.parse( rxnfile, metabolitefile )
fluxModel = FluxModel( network )
fluxLimits = {}
objective = {}
analysis_names = []
fluxLimitParser = FluxLimitFlatFileParser()
objectiveParser = ObjectiveFlatFileParser()
for analysisName in analysisNames:
fluxlimitfile = fluxlimitfiles[analysisName]
objectivefile = objectivefiles[analysisName]
fluxLimits= fluxLimitParser.parse( fluxlimitfile )
objective= objectiveParser.parse( objectivefile )
fluxModel.addAnalysis( analysisName, objective, fluxLimits )
return fluxModel