posE = pos
# select samples
sample_charaters = calls.selectSamples(sampCol, words)
# check if one- or two-character code
if any(["/" in gt for gt in sample_charaters]):
sample_charaters = calls.twoToOne(sample_charaters)
# if window size is reached output the results
if Chr > ChrPrevious: # if end of a chromosome
try:
HeterWindow = round(meanWindow(Hwindow, Twindow), 4)
except Exception:
HeterWindow = "NA"
calls.processWindow(ChrPrevious, posS, posE, HeterWindow,
outputFile)
windPosEnd = windSize
Hwindow = []
Twindow = []
posS = pos
elif pos > windPosEnd: # if end of a window
try:
HeterWindow = round(meanWindow(Hwindow, Twindow), 4)
except Exception:
HeterWindow = "NA"
calls.processWindow(Chr, posS, posE, HeterWindow, outputFile)
windPosEnd = windPosEnd + windSize
Hwindow = []
Twindow = []
posS = pos
while pos > windPosEnd: # if the gap in positions is larger than window size
pos = int(words[1])
indVal = float(words[2])
# to store the values of a previous line
if not ChrPrevious:
ChrPrevious = Chr
if not posS:
posS = pos
if not posE:
posE = pos
# if window size is reached output the results
if Chr != ChrPrevious: # if end of a chromosome
meanValWindow = proportionWindow(Vwindow, args.threshold)
meanValWindowP = '\t'.join(str(s) for s in meanValWindow)
calls.processWindow(ChrPrevious, posS, posE, meanValWindowP,
outputFile)
windPosEnd = windSize
Vwindow = []
posS = pos
elif pos > windPosEnd: # if end of a window
if Vwindow:
meanValWindow = proportionWindow(Vwindow, args.threshold)
meanValWindowP = '\t'.join(str(s) for s in meanValWindow)
calls.processWindow(Chr, posS, posE, meanValWindowP,
outputFile)
windPosEnd = windPosEnd + windSize
Vwindow = []
posS = pos
while pos > windPosEnd: # gap is larger than window size
windPosEnd = windPosEnd + windSize
# to store the values of a previous line
if not ChrPrevious:
ChrPrevious = Chr
if not posS:
posS = pos
if not posE:
posE = pos
# select samples
sample_charaters = calls.selectSamples(sampCol, words)
# if window size is reached output the results
if Chr > ChrPrevious:
NsInWindow = meanInWindow(Nwindow, nSample)
calls.processWindow(ChrPrevious, posS, posE, NsInWindow,
NsFr_output)
windPosEnd = windSize
Nwindow = []
posS = pos
elif pos > windPosEnd:
NsInWindow = meanInWindow(Nwindow, nSample)
calls.processWindow(Chr, posS, posE, NsInWindow, NsFr_output)
windPosEnd = windPosEnd + windSize
Nwindow = []
posS = pos
while pos > windPosEnd: # if the gap in positions is larger than window size
windPosEnd = windPosEnd + windSize
ChrPrevious = Chr
posE = pos