'''start thread for writing the results'''
worker = Thread(target=writer, args=(writeQueue, outFile, args.verbose,))
worker.daemon = True
worker.start()
'''start background Thread that will run a loop to check run statistics and print
We use thread, because I think this is necessary for a process that watches global variables like linesTested'''
worker = Thread(target=checkStats)
worker.daemon = True
worker.start()
########################################################################################################################
#generate windows and queue
windowGenerator = genomics.nonOverlappingSitesWindows(genoFile, args.windSize,names=sampleData.indNames,
include = scafsToInclude,exclude = scafsToExclude)
if not args.test:
for window in windowGenerator:
windowQueue.put((windowsQueued,window))
windowsQueued += 1
else:
for window in windowGenerator:
windowQueue.put((windowsQueued,window))
windowsQueued += 1
if windowsQueued == 10: break
############################################################################################################################################
if args.genoFile:
genoFile = gzip.open(args.genoFile,"r") if args.genoFile.endswith(".gz") else open(args.genoFile, "r")
else:
assert args.prefix != None, "Please povide a prefix for the ouput files"
genoFile = sys.stdin
#########################################################################################
###################### read data ####################################################
#we will make a list of geno windows for each scaffold
scafWindows = []
for i, window in enumerate(genomics.nonOverlappingSitesWindows(genoFile, windSites=np.inf,names=args.samples)):
scafWindows.append(window)
sys.stderr.write("{} scaffolds read into memory\n".format(i+1))
genoFile.close()
#make concatenated sequences for each sample
names = scafWindows[0].names
sampleSeqs = defaultdict(list)
for scafWindow in scafWindows:
windowSeqs = scafWindow.seqDict()
for name in names:
sampleSeqs[name] += [a for pair in zip(*genomics.splitSeq(windowSeqs[name],genoFormat=args.genoFormat)) for a in pair]