def readAnnotatedTargets(self,targetFile,model,annotationName,regex,bNames = False,orderGenes = False):
parser = FlatFileParser()
modelFactory = ModelFactory()
modelFactory.orderGenes = orderGenes
report = parser.parseToReport(targetFile, "Row Names", header=["Control","Flux","Reaction Control","Flux Changes"])
controlValues = report.getColumn("Control")
if bNames:
controlValues = self._deannotateGenes(controlValues, model, annotationName, regex)
if self.orderGenes:
controlValues = modelFactory.refactorStringMap(controlValues, sep="_")
controlScore = report.getColumn("Flux")
if bNames:
controlScore = self._deannotateGenes(controlScore, model, annotationName, regex)
return(controlValues,controlScore)
def loadControlTable(fileName,keyTag="Row Names",controlTag="control values",productionTag = "production"):
'''
Load flat file of control designs and production values
'''
if not os.path.exists(fileName):
print "file name not found %s" % (fileName)
return ([],None)
header = [keyTag,controlTag,productionTag]
parser = FlatFileParser()
report = parser.parseToReport(fileName, keyTag=keyTag, header=header)
result = []
for rowName in report.returnRowNames():
controlMapString = report.get(rowName, controlTag)
controlMap = eval(controlMapString)
production = report.get(rowName, productionTag)
controlMapValue = (controlMap,production)
result.append(controlMapValue)
return (result,report)
def loadTargetTable(fileName,keyTag="Row Names",controlTag="control values"):
'''
Load flat file of control targets
'''
if not os.path.exists(fileName):
#print "file name not found %s" % (fileName)
return ({},None)
else:
pass
#print "parsing %s" % (fileName)
header = [keyTag,controlTag]
parser = FlatFileParser()
report = parser.parseToReport(fileName, keyTag=keyTag, header=header)
controlMap = {}
for rowName in report.returnRowNames():
keyName= rowName
controlValue = report.get(rowName, controlTag)
controlMap[keyName] = controlValue
return (controlMap,report)
def parseUserTargets(controlFile,model):
parser = FlatFileParser()
gtMap = model.getGeneTargetMap()
report = parser.parseToReport(controlFile, "GeneName", header=["GeneName","library","prefix","bnumber","value"])
rowNames = report.returnRowNames()
controlNames = []
controlIds = set()
controlLibrariesMap = {}
for rowName in rowNames:
libName = report.getElement(rowName, "library")
prefix = report.getElement(rowName, "prefix")
geneID = report.getElement(rowName, "bnumber")
value = report.getElement(rowName, "value")
rxnControlMap = {}
geneID = geneID.replace(" ","_")
if geneID not in gtMap.keys():
continue
for rxn in gtMap[geneID]:
rxnControlMap[rxn] = value
controlID = (libName,prefix,geneID)
controlNames.append(geneID)
controlIds.add(controlID)
if (libName,prefix) not in controlLibrariesMap.keys():
controlLibrariesMap[(libName,prefix)] = {}
controlLibrariesMap[(libName,prefix)].update(rxnControlMap)
controlLibraries =[]
for (key,value) in controlLibrariesMap.items():
(libName,prefix) = key
controlLibraries.append((libName,prefix,value))
return (controlNames,controlIds,controlLibraries)
#------------------------
targetTag = "([^ACGTacgt]+.*[^ACGTacgt]+)"
boundary = options.flankingSize
#boundary = 45
searchSize = 200
cutOff = (None,-13.0)
primerSize = 20
primerTm = 58
primerDistance = 250
#--------------------------
#Start factories
#--------------------------
fileParser = FlatFileParser()
seqTools = SequenceTools()
seqTools.verbose = verbose
seqFac = SequenceFactory()
seqFac.verbose = verbose
recFac = RecombinationOligoFactory()
recFac.verbose = verbose
oligoRecords = None
gRecord = None
#----------------------------------
# Generate new oligos from targets
#----------------------------------
if mode == "location" or (locationFile != '' and mode == "auto"):
