#oligoSeqFile = options.workFolder + oligoSeqFile
#bTools = BlastTools()
#bTools.verbose = verbose
#bTools.blastDB = blastDB
#bTools.blastExe = blastExe
if rregx != None:
readTag = rregx.group(1).replace(".","_")
else:
readTag = "read_analysis"
readRecord = parseVCFFile(readFile)
targetRecords= SeqIO.parse(open(targetFile), "fasta")
targetRecords = list(targetRecords)
print "Processing [%s] records" % (len(targetRecords))
if verbose: print "blasting sequences"
seqTools = SequenceTools()
seqTools.verbose = verbose
blastedFeatures = seqTools.seqBlastToFeatures(blastDB, blastExe, targetFile, blastType = "blastn",scoreMin = 1e-5)
if verbose: print "finished blasting locations"
readLogName = "read_log_%s.txt" % (readTag)
logFile = open(readLogName,"w")
alignmentReport = annotateAlignment(readRecord, blastedFeatures,logFile=logFile)
logFile.close()
print "Done"
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"):
controlRegionTools = ControlRegionTools()
