def writeAnnotatedTargets(self,objective,model,annotationName,regex,iteration,oPrediction={},nPrediction={},outputFileName=None):
if outputFileName == None:
outputFileName = "Target_Report_T_%s_C_%s_M_%s_N_%s_S_%s_K_%s_I_%s.txt" % (self.resultTag,self.control,self.modelName,self.naturalObjectiveName,self.syntheticObjectiveName,self.con.controlMax,iteration)
aValue = self._annotateObjective(objective, model, annotationName, regex)
controlValues = self._condenseObjective(objective)
controlValues = self._annotateGenes(controlValues, model, annotationName, regex)
controlScores = self._controlScore(objective,oPrediction, nPrediction)
controlScores = self._annotateGenes(controlScores, model, annotationName, regex)
controlScore = self._condenseMap(controlScores,sum)
report = Report()
report.addColumnHash("Control", aValue)
report.addColumnHash("Flux", controlScore)
report.addColumnHash("Reaction Control", controlValues)
report.addColumnHash("Flux Changes", controlScores)
oName = self.resultDirectory + outputFileName
try:
writer = ReportWriter()
writer.setFile(oName)
writer.write(report)
writer.closeFile()
if self.verbose: print "Report written [%s]" % (outputFileName)
except:
if self.verbose: print "Failed to write report [%s] " % (outputFileName)
return None
def writeReport(self,ltReport,fluxModel, oPredVal,sPredVal,s2PredVal,neighborhood,iterations,fObjective,resultDir):
if self.verbose: print "Preparing report ..."
report = Report()
reactionNames = fluxModel.network.getOrderedReactionNames()
reactionMap = fluxModel.network.getReactionMap()
for reactionName in reactionNames:
reaction = reactionMap[reactionName]
equation = reaction.getEquation()
pathway = reaction.getAnnotation("Subsystem")
name = reaction.getName()#Currently sensitivity values can be too large for control factors.
report.addElement(reactionName,"name",name)
report.addElement(reactionName,"equation", equation)
report.addElement(reactionName,"Subsystem", pathway)
#--------------------
#Analysis in report
#--------------------
report.addColumnHash("Original", oPredVal)
report.addColumnHash("Synthetic", sPredVal)
report.addColumnHash("Synthetic mBio", s2PredVal)
report.extend(ltReport)
report.addColumnHash("Final Objective", fObjective)
#--------------------
#Write Report
#--------------------
if self.verbose: print "Writing report ..."
outputFileName = resultDir + "RD_" + self.resultTag + "_" + self.modelName + "_" + self.syntheticObjectiveName + "_" + str(neighborhood) + "_" + str(iterations) + "_" + strftime('%Y%m%dT%H%M%S') + ".txt"
writer = ReportWriter()
writer.setFile(outputFileName)
writer.write(report)
writer.closeFile()
if self.verbose: print "Report Written [%s]" % (outputFileName)
return report
