windSize,
stepSize,
sampleData.indNames,
include=scafsToInclude,
exclude=scafsToExclude)
elif windType == "sites":
windowGenerator = genomics.slidingSitesWindows(genoFile,
windSize,
overlap,
maxDist,
minSites,
sampleData.indNames,
include=scafsToInclude,
exclude=scafsToExclude)
else:
windowGenerator = genomics.predefinedCoordWindows(genoFile, windCoords,
sampleData.indNames)
for window in windowGenerator:
windowQueue.put((windowsQueued, window))
windowsQueued += 1
############################################################################################################################################
print >> sys.stderr, "\nWriting final results...\n"
while resultsHandled < windowsQueued:
sleep(1)
sleep(5)
genoFile.close()
outFile.close()
names=args.columns,
include=scafsToInclude,
exclude=scafsToExclude)
elif windType == "sites":
windowGenerator = genomics.slidingSitesWindows(inFile,
windSize,
overlap,
maxDist,
minSites,
headerLine=args.header,
names=args.columns,
include=scafsToInclude,
exclude=scafsToExclude)
else:
windowGenerator = genomics.predefinedCoordWindows(inFile,
windCoords,
headerLine=args.header,
names=args.columns)
n = 0
for window in windowGenerator:
#if its the first window, get the headings and write
if n == 0:
for name in window.names:
outFile.write("," +
",".join([name + "_" + stat for stat in args.stats]))
outFile.write("\n")
if windType == "coordinate" or windType == "predefined":
scaf, start, end, mid, sites = (window.scaffold, window.limits[0],
window.limits[1], window.midPos(),
exclude=scafsToExclude)
elif args.windType == "sites":
windowGenerator = genomics.slidingSitesWindows(
genoFile,
windSize,
overlap,
maxDist,
minSites,
headerLine=headerLine,
names=sampleData.indNames,
include=scafsToInclude,
exclude=scafsToExclude)
else:
windowGenerator = genomics.predefinedCoordWindows(
genoFile,
windCoords,
headerLine=headerLine,
names=sampleData.indNames)
for window in windowGenerator:
windowQueue.put((windowsQueued, window))
windowsQueued += 1
############################################################################################################################################
while resultsHandled < windowsQueued:
sleep(1)
sleep(5)
genoFile.close()
windSize,
stepSize,
columns,
include=scafsToInclude,
exclude=scafsToExclude)
elif windType == "sites":
windowGenerator = genomics.slidingSitesWindows(inFile,
windSize,
overlap,
maxDist,
minSites,
columns,
include=scafsToInclude,
exclude=scafsToExclude)
else:
windowGenerator = genomics.predefinedCoordWindows(inFile, windCoords,
columns)
n = 0
for window in windowGenerator:
#if its the first window, get the headings and write
if n == 0:
for name in window.names:
outFile.write("," + ",".join([
name + "_mean", name + "_median", name + "_max", name +
"_min", name + "_sd"
]))
outFile.write("\n")
if windType == "coordinate" or windType == "predefined":
scaf, start, end, mid, sites = (window.scaffold, window.limits[0],
stepSize,
indNames,
include=scafsToInclude,
exclude=scafsToExclude)
elif windType == "sites":
windowGenerator = genomics.slidingSitesWindows(genoFile,
windSize,
overlap,
maxDist,
minSites,
indNames,
include=scafsToInclude,
exclude=scafsToExclude)
else:
windowGenerator = genomics.predefinedCoordWindows(genoFile,
windCoords,
names=indNames)
for window in windowGenerator:
#simpleque has no max, so to make sure we haven't gotten ahead of ourselves, we compare windowsQueued to resultsReceived
while windowsQueued - resultsReceived >= 50:
sleep(10)
if test or verbose: sys.stderr.write("Waiting for queue to clear...\n")
if test or verbose:
if test: sleep(0.5)
sys.stderr.write("Sending window {} to queue. Length: {}\n".format(
windowsQueued, window.seqLen()))
windowQueue.put((windowsQueued, window))
windowsQueued += 1
##########################################################
#get windows and analyse
if windType == "coordinate": windowGenerator = genomics.slidingCoordWindows(genoFile, windSize, stepSize,
headerLine = args.header,
names = sampleData.indNames,
include = scafsToInclude,
exclude = scafsToExclude)
elif windType == "sites": windowGenerator = genomics.slidingSitesWindows(genoFile, windSize, overlap,
maxDist, minSites,
headerLine = args.header,
names = sampleData.indNames,
include = scafsToInclude,
exclude = scafsToExclude)
else: windowGenerator = genomics.predefinedCoordWindows(genoFile, windCoords,
headerLine = args.header
names = sampleData.indNames)
for window in windowGenerator:
windowQueue.put((windowsQueued,window))
windowsQueued += 1
############################################################################################################################################
print("Writing final results...", file=sys.stderr)
while resultsHandled < windowsQueued:
sleep(1)
sleep(5)
