#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()