derived = gtS[0]
gtS[0] = '1'
gtS[1] = '0'
elif (gtS[0] not in ances_gt) and (gtS[1] not in ances_gt):
if gtS[0] == gtS[1]:
derived = gtS[0]
else:
derived = '/'.join(str(e) for e in gtS)
gtS[0] = '1'
gtS[1] = '1'
elif (gtS[0] in ances_gt) and (gtS[1] in ances_gt) and
gtS[0] != gtS[1]:
gtS = random.choice([['0', '1'], ['1', '0']])
else:
raise IOError('Unexpected case: Ancestral:%s, GT:%s '
'in %s %s' %
(ances_gt, gtS, words[0], words[1]))
gtSP = '/'.join(str(e) for e in gtS)
samples_gtPlarized.append(gtSP)
if all('./.' in gt for gt in samples_gtPlarized) or derived == 'N':
continue
else:
wordsP = '\t'.join(str(e) for e in samples_gtPlarized)
output.write('%s\t%s\t%s\t%s\t%s\n' %
(words[0], words[1], ances_words[2], derived, wordsP))
counter = calls.lineCounter(counter)
datafile.close()
ances.close()
output.close()
print('Done!')
halfWindow = float(windows_step) / 2
with open(args.input) as datafile:
datafile.readline()
for line in datafile:
words = line.split()
CHRcurrent = words[0]
POScurrent = int(words[1])
if CHRprev != CHRcurrent:
if numberSNPs != 'NA':
POS = int(windowsEnd - halfWindow)
processWindow(CHRprev, POS, numberSNPs, output)
numberSNPs = 1
windowsEnd = windows_step
elif POScurrent > windowsEnd:
POS = int(windowsEnd - halfWindow)
processWindow(CHRprev, POS, numberSNPs, output)
numberSNPs = 1
windowsEnd += windows_step
else:
numberSNPs += 1
CHRprev = CHRcurrent
POSprev = POScurrent
lineNumber = calls.lineCounter(lineNumber)
POS = int(windowsEnd - halfWindow)
processWindow(CHRprev, POS, numberSNPs, output)
print 'Done!'