##########################################################
#get windows and analyse
if windType == "coordinate":
windowGenerator = genomics.slidingCoordWindows(genoFile,
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:
#get windows and analyse
if windType == "coordinate":
windowGenerator = genomics.slidingCoordWindows(inFile,
windSize,
stepSize,
headerLine=args.header,
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:
if args.windType == "cat":
window = genomics.parseGenoFile(genoFile, headerLine = args.header, names=sampleData.indNames)
windowQueue.put((windowsQueued,window))
windowsQueued += 1
else:
#get windows and analyse
if args.windType == "coordinate": windowGenerator = genomics.slidingCoordWindows(genoFile, windSize, stepSize,
headerLine = args.header,
names = sampleData.indNames,
include = scafsToInclude,
exclude = scafsToExclude)
elif args.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
############################################################################################################################################
while resultsHandled < windowsQueued:
sleep(1)
##########################################################################################################
#get windows and analyse
if windType == "coordinate":
windowGenerator = genomics.slidingCoordWindows(inFile,
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 +
windSize = 1e7
minSites = 1
stepSize = 1e7
#initialise window generator
if windType == "coordinate":
windowGenerator = genomics.slidingCoordWindows(
genoFile,
windSize,
stepSize,
args.samples,
splitPhased=args.splitPhased)
else:
windowGenerator = genomics.slidingSitesWindows(
genoFile,
windSize,
overlap,
maxDist,
minSites,
args.samples,
splitPhased=args.splitPhased)
for window in windowGenerator:
posString = str(window.firstPos()) + "_" + str(window.lastPos())
#open file if necessary
if args.separateFiles:
if args.format == "fasta": ext = ".fa"
else: ext = ".phy"
seqFileName = args.seqFile + "." + window.scaffold
if args.mode == "windows": seqFileName += "_" + posString
seqFileName += ext
