def main(inFilePath,outFilePath):
(exnH, totalLen) = loadExonH()
depthH = {'0':{}, '15':{}, '20':{}, '30':{}}
exnChr = 'chr1'
exnIdx = 0
if inFilePath[-3:] == '.gz':
inFile = gzip.open(inFilePath, 'rb')
else:
inFile = open(inFilePath)
for line in inFile:
tokL = line.split('\t')
chrom, pos, cnt = tokL[0], int(tokL[1]), int(tokL[3])
if chrom==exnChr and exnIdx==len(exnH[exnChr]):
continue
if chrom != exnChr:
exnChr = chrom
exnIdx = 0
while exnIdx < len(exnH[exnChr]) and exnH[exnChr][exnIdx][1] < pos:
exnIdx += 1
if exnIdx < len(exnH[exnChr]) and exnH[exnChr][exnIdx][0] < pos <= exnH[exnChr][exnIdx][1]:
for dt in ['0', '15', '20', '30']:
cnt = get_cnt_by_qual(line, int(dt))
if cnt > 1000:
mybasic.incHash(depthH[dt], 1001, 1)
else:
mybasic.incHash(depthH[dt], cnt, 1)
for dt in ['0','15','20','30']:
depthH[dt][0] = totalLen - sum(depthH[dt].values())
for dt in ['0','15','20','30']:
outFile = open(outFilePath + '_mq' + dt, 'w')
# for i in range(max(depthH[dt].keys())+1):
for i in range(1001):
if i in depthH[dt]:
d = depthH[dt][i]
else:
d = 0
outFile.write('%d\t%d\n' % (i,d))
if 1001 in depthH[dt]:
outFile.write('1001\t%d\n' % depthH[dt][1001])
else:
outFile.write('1001\t0\n')
outFile.flush()
outFile.close()
dir = '/'.join(outFilePath.split('/')[:-1])
sampN = outFilePath.split('/')[-1].split('.')[0]
os.system('R --no-restore --no-save --args %s %s < %s/NGS/quality/plot_depth.R' % (dir, sampN, mysetting.SRC_HOME))
def main(inFilePath,outFilePath):
exnH = loadExonH()
depthH = {}
exnChr = 'chr10'
exnIdx = 0
inFile = open(inFilePath)
outFile = open(outFilePath,'w')
for line in inFile:
tokL = line.split(':')
chrom, pos, cnt = tokL[0], int(tokL[1]), int(tokL[3])
if chrom==exnChr and exnIdx==len(exnH[exnChr]):
continue
if chrom != exnChr:
exnChr = chrom
exnIdx = 0
while exnH[exnChr][exnIdx][1] < pos:
exnIdx += 1
if exnIdx == len(exnH[exnChr]):
break
if exnIdx < len(exnH[exnChr]) and exnH[exnChr][exnIdx][0] < pos <= exnH[exnChr][exnIdx][1]:
mybasic.incHash(depthH,cnt,1)
for :
def main(inFilePath, outFilePath):
(exnH, totalLen) = loadExonH()
depthH = {'0': {}, '15': {}, '20': {}, '30': {}}
exnChr = 'chr1'
exnIdx = 0
if inFilePath[-3:] == '.gz':
inFile = gzip.open(inFilePath, 'rb')
else:
inFile = open(inFilePath)
for line in inFile:
tokL = line.split('\t')
chrom, pos, cnt = tokL[0], int(tokL[1]), int(tokL[3])
if chrom == exnChr and exnIdx == len(exnH[exnChr]):
continue
if chrom != exnChr:
exnChr = chrom
exnIdx = 0
while exnIdx < len(exnH[exnChr]) and exnH[exnChr][exnIdx][1] < pos:
exnIdx += 1
if exnIdx < len(
exnH[exnChr]
) and exnH[exnChr][exnIdx][0] < pos <= exnH[exnChr][exnIdx][1]:
for dt in ['0', '15', '20', '30']:
cnt = get_cnt_by_qual(line, int(dt))
if cnt > 1000:
mybasic.incHash(depthH[dt], 1001, 1)
else:
mybasic.incHash(depthH[dt], cnt, 1)
for dt in ['0', '15', '20', '30']:
depthH[dt][0] = totalLen - sum(depthH[dt].values())
for dt in ['0', '15', '20', '30']:
outFile = open(outFilePath + '_mq' + dt, 'w')
# for i in range(max(depthH[dt].keys())+1):
for i in range(1001):
if i in depthH[dt]:
d = depthH[dt][i]
else:
d = 0
outFile.write('%d\t%d\n' % (i, d))
if 1001 in depthH[dt]:
outFile.write('1001\t%d\n' % depthH[dt][1001])
else:
outFile.write('1001\t0\n')
outFile.flush()
outFile.close()
dir = '/'.join(outFilePath.split('/')[:-1])
sampN = outFilePath.split('/')[-1].split('.')[0]
os.system(
'R --no-restore --no-save --args %s %s < %s/NGS/quality/plot_depth.R' %
(dir, sampN, mysetting.SRC_HOME))