Example #1
0
 def generateLongNameReport(self,fluxModel):
     report = Report()
     for name in fluxModel.getMetabolicNetwork().getOrderedReactionNames():
         reaction = fluxModel.getMetabolicNetwork().getReaction(name)
         longName = reaction.getName()
         equation = reaction.getEquation()
         report.addElement(name,"LongName",longName)
         report.addElement(name,"Equation",equation)
     return report
Example #2
0
 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