fastaFile = PipMethod.rstrip()[:-3]+"fa"
PrimerDesign.PrimerDesign.saveFasta(fastaFile, PrimerDesign.PrimerDesign.readGFF(PipMethod, genome))
blastList.append(fastaFile)
otherGenomes = copy.copy(Main.Main.refGenomeList)
del otherGenomes[0]
blastThread = list()
allAlias = ""
for genome in otherGenomes:
Blast.makeDatabase(str(genome), Main.Main.workDir)
allAlias += Main.Main.workDir + "/" + genome + " "
allAlias = allAlias.rstrip()
Blast.aliasTool(allAlias, Main.Main.workDir)
for blastItem in blastList:
blastResult = Blast(blastItem, otherGenomes)
blastResult.start()
blastThread.append(blastResult)
for blastItem in blastThread:
blastItem.join()
genome = PrimerDesign.PrimerDesign.readRefGenome(Main.Main.genomeAdd + Main.Main.refGenomeList[0])
for k, blastItem in enumerate(blastList):
item = blastItem.rstrip()[:-2]
thread = threading.Thread(PrimerDesign.PrimerDesign.generatePrimer3Input(
item+"primSets", PrimerDesign.PrimerDesign.readGFF(item+"unique.gff", genome)))
thread.start()
Main.Main.threadList.append(thread)
for thread in Main.Main.threadList:
thread.join()
