def scanControlDependencies(con,originalModel,controls,options,searchRange,targetPrecent = 0.80,verbose = False): report = Report() controlMaps = [] controlSets = set() for z in searchRange: (controlMap,controlSet,iReport) = findControlDependencies(con,originalModel,controls,controlSets,options,z,targetPrecent,verbose) controlSets = controlSets.union(controlSet) controlMaps.extend(controlMap) report.extend(iReport) return (controlMaps,report)
def generateReport(self,fluxModel, modelName, predictions, limits = False, longName = False,): result = Report() if longName: longNamesReport = self.generateLongNameReport(fluxModel) result.extend(longNamesReport) result.addReportColumnHash("FluxPrediction",predictions) if limits: limits = fluxModel.getLimits(modelName) limitReport = self.generateLimitReport(limits) result.extend(limitReport) return result
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
seqRegions = [] for (id,location) in targetMap.items(): low = location - 300 high = location + 300 iSeq = seqData[low:high] isRecord = SeqRecord(iSeq,id=id) seqRegions.append(isRecord) sRegionHandel = open("OligoSequenceRegions.fasta","w") SeqIO.write(seqRegions,sRegionHandel,"fasta") sRegionHandel.close() seqTools = SequenceTools() seqTools.verbose = verbose primerReport = seqTools.findPrimers(seqData, targetMap, boundary=primerDistance, oligoSize=primerSize, searchSize=60, targetTm=primerTm) report.extend(primerReport) #---------------------------- # Write Report #---------------------------- writer = ReportWriter() writer.setFile(oligoFileName) writer.write(report) writer.closeFile() #----------------------------------------- # do comparison of recombination oligos # to sequecing of strains #----------------------------------------- if mode == "sequence" or (mode == "auto" and recSeqFileName != ''):