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 != ''):
