def loadVariousControlTable(fileNameTag,controls,sObjectiveTags,k,n,filter=lambda x: True):
'''
Parse control table files
'''
keyTag = "Row Names"
controlTag = "Control"
productionTag = ''
#bestTargets = 'accA,fadD,fadE'.split(",")
#bestTargets = 'aceE,fabH,fabD,accA,fabA,fabZ,fabB,fabF,fadA,fadI,fadB,fadD'.split(",")
#mTargets = "pgi,pfkA,eno,fbaA,tpiA,gapA,pgk,gpmA".split(",")
#bestTargets.extend(mTargets)
bestTargets = 'accA,lpdA,aceE,aceF,gapA,pgk,fumB,fumC,mdh,acnA,scpC,sucC,sucD,sdhA,sdhB'.split(",")
#bestTargets = 'lpdA,aceE,aceF,'.split(",")
summaryReport = Report()
targetReport = Report()
print "best targets %s" % (bestTargets)
for sObjective in sObjectiveTags:
controlMaps = loadControlTableRange(fileNameTag, controls, sObjective, k, n, keyTag, controlTag, productionTag,filter)
(uniqueTargets,targetValues,maxTargetSize,(bestMaps,score)) = processControlMaps(controlMaps, minProduction=0.0,bestTargets=bestTargets)
print "Production %s => %s" % (sObjective,score)
for map in bestMaps:
print "%s" % (map)
uTargetSize = len(uniqueTargets)
summaryReport.add(sObjective, "Unique Target Number", uTargetSize)
summaryReport.add(sObjective, "Largest Design", maxTargetSize)
for (key,value) in targetValues.items():
targetReport.add(key, sObjective, value)
return (summaryReport,targetReport)
def findControlDependencies(con,originalModel,controls,exclusion,options,searchSize=0,targetPrecent = 0.40,verbose = False,usePersist=False):
name = "".join(originalModel.modelName)
naturalObjectiveName = options.bioObj
syntheticObjectiveName = options.synthObj
controlTag = options.control
persistTag = "Dependency_persist_%s_%s_%s_%s_%s_%s" % (controlTag,name,naturalObjectiveName,syntheticObjectiveName,str(searchSize),str(targetPercent))
delta = 1e-4
iter = 0
iterSave = 100
completed = set()
controlSet = set()
controlMap = []
report = Report()
persistValue = None
if usePersist:
persistValue = loadPersist(persistTag)
if persistValue != None:
print "loading persisted dependency search"
(completed,controlMap,controlSet,report) = persistValue
controlSubSets = combinations(controls,searchSize)
xcontrolSubSets = set(controlSubSets)
xcontrolSubSets = xcontrolSubSets.difference(completed)
print "Control dependency depth [%s] search sets [%s]" % (searchSize,len(xcontrolSubSets))
lo = LPSolver()
sObjective = {syntheticObjectiveName:-1.0}
iPred = lo.run(model= originalModel, objective = sObjective)
synthVal = iPred[syntheticObjectiveName]
targetSVal = synthVal * targetPrecent
#print "Synthetic Target [%s] = %s * %s" % (targetSVal,synthVal,targetPercent)
controlMin = con.controlMin
controlMax = con.controlMax
con.controlMin = 0
con.controlMax = 0
targets = []
gRMap = con.getGeneTargetMap()
for (lib,prefix,target) in controls:
if gRMap != None:
if target in gRMap.keys():
rTargets = gRMap[target]
targets.extend(rTargets)
else:
targets.append(target)
#-----------------------------
# Run optimization
#-----------------------------
iter = 0
for controlSub in xcontrolSubSets:
iter += 1
completed.add(controlSub)
#Analysis of control
(prediction,objective) = simpleTestOpt(con, originalModel, controlSub, naturalObjectiveName,syntheticObjectiveName,verbose=False,naturalCoefficient=-0.5)
#Save results
syntheticFlux = prediction[syntheticObjectiveName]
#if verbose: print "Objective [%s]" % (objective)
#if verbose: print "Flux [%s]" % (prediction)
if syntheticFlux > targetSVal:
controlThresholds = controlThreshold([controlSub], exclusion)
if controlSub in controlThresholds.keys():
if syntheticFlux <= controlThresholds[controlSub] + delta:
#if verbose: print "no improvement"
continue
if verbose: print "Synthetic Production [%s]" % (syntheticFlux)
controlResultMap = originalModel.annotateGenes(objective,annotationName = "bnumber", regex="[a-zA-Z0-9\(\)]+")
controlTag = str(controlResultMap.keys())
controlSV = (controlSub,syntheticFlux)
controlSet.add(controlSV)
controlSV = (controlResultMap,syntheticFlux)
controlMap.append(controlSV)
#if verbose: print "Control Set [%s]" % (controlSub)
if verbose: print "Control Map [%s]" % (controlResultMap)
report.add(controlTag, "control values", controlResultMap)
report.add(controlTag, "production", syntheticFlux)
if iter % iterSave == 0:
print "persisting iteration %s" % (iter)
persistValue = (completed, controlSet,controlMap, report)
persist(persistTag, persistValue)
con.controlMin = controlMin
con.controlMax = controlMax
#Persist dependency search
if usePersist:
persistValue = (completed, controlSet,controlMap, report)
persist(persistTag, persistValue)
return (controlMap,controlSet,report)