def main(inFileName, outFileName, inRefFlatFileName='/data1/Sequence/ucsc_hg19/annot/refFlat.txt', assembly='hg19'):
geneNameL = list(set([line.split('\t')[0] for line in open(inRefFlatFileName)]))
geneNameL.sort()
inFileL = [line[:-1].split('\t') for line in open(inFileName) if line[:-1].split('\t')[0] != 'ID']
outFile = open(outFileName, 'w')
for geneName in geneNameL:
try:
trans = mygenome.transcript(geneName,inRefFlatFileName,assembly)
except:
continue
for dataL in inFileL:
(sId, chrNum, chrSta, chrEnd, type, cn) = dataL
overlap = trans.cdsOverlap((chrNum,int(chrSta),int(chrEnd)))
if overlap > 0:
if type != 'gain':
outFile.write('%s\t%s\t%s\n' % (sId,geneName,type))
def main(inFileName,
outFileName,
inRefFlatFileName='/data1/Sequence/ucsc_hg19/annot/refFlat.txt',
assembly='hg19'):
geneNameL = list(
set([line.split('\t')[0] for line in open(inRefFlatFileName)]))
geneNameL.sort()
inFileL = [
line[:-1].split('\t') for line in open(inFileName)
if line[:-1].split('\t')[0] != 'ID'
]
outFile = open(outFileName, 'w')
for geneName in geneNameL:
try:
trans = mygenome.transcript(geneName, inRefFlatFileName, assembly)
except:
continue
for dataL in inFileL:
(sId, chrNum, chrSta, chrEnd, type, cn) = dataL
overlap = trans.cdsOverlap((chrNum, int(chrSta), int(chrEnd)))
if overlap > 0:
if type != 'gain':
outFile.write('%s\t%s\t%s\n' % (sId, geneName, type))
def main(inSegFileName, inRefFlatFileName, outFileName, geneNameL, assembly='hg19'):
#sampN = re.match('(.*).ngCGH.seg', inSegFileName.split('/')[-1]).group(1)
(sid, postfix) = re.match('(.*)_([TXC].{,2})_.*.ngCGH.seg', inSegFileName.split('/')[-1]).groups()
if postfix != 'T':
sampN = sid + '_' + postfix
else:
sampN = sid
if geneNameL == []:
geneNameL = list(set([line.split('\t')[0] for line in open(inRefFlatFileName)]))
geneNameL.sort()
inSegFileMem = [line[:-1].split('\t') for line in open(inSegFileName) if line[:-1].split('\t')[0] != 'ID']
sIdL = list(set([tokL[0] for tokL in inSegFileMem]))
sIdL.sort()
outFile = open(outFileName, 'w')
for geneName in geneNameL:
print geneName
try:
trans = mygenome.transcript(geneName,inRefFlatFileName,assembly)
except:
continue
h = {}
for sId in sIdL:
h[sId] = 0.
for tokL in inSegFileMem:
(sId,chrNum,chrSta,chrEnd,numMarker,value) = tokL
if 'chr' in chrNum:
chrNum = re.match('chr(.*)', chrNum).group(1)
if chrNum != trans.chrNum or value in ('NA','null','NULL'):
continue
overlap = trans.cdsOverlap((chrNum,int(chrSta),int(chrEnd)))
if overlap > 0:
h[sId] += overlap/float(trans.cdsLen) * float(value)
outFile.write('%s\t%s' % (sampN, geneName))
for sId in sIdL:
outFile.write('\t%s' % h[sId])
outFile.write('\n')
sIdL = list(set([tokL[0] for tokL in inSegFileMem]))
sIdL.sort()
outGctFileName = '%s.gct' % mygp.stripPath(inSegFileName)[0]
outGctFile = open(outGctFileName,'w')
outGctFile.write('#1.2\n')
outGctFile.write('%s\t%s\n' % (len(geneNameL),len(sIdL)))
outGctFile.write('NAME\tDescription\t%s\n' % '\t'.join(sIdL))
for geneName in geneNameL:
print geneName
trans = mygenome.transcript(geneName,inRefFlatFileName,'hg18') # consider only the longest transcript per gene
h = {}
for sId in sIdL:
h[sId] = 0.
for tokL in inSegFileMem:
(sId,chrNum,chrSta,chrEnd,numMarker,value) = tokL
if chrNum != trans.chrNum or value in ('NA','null','NULL'):
continue
overlap = trans.cdsOverlap((chrNum,int(chrSta),int(chrEnd)))
sIdL = list(set([tokL[0] for tokL in inSegFileMem]))
sIdL.sort()
outGctFileName = '%s.gct' % mygp.stripPath(inSegFileName)[0]
outGctFile = open(outGctFileName, 'w')
outGctFile.write('#1.2\n')
outGctFile.write('%s\t%s\n' % (len(geneNameL), len(sIdL)))
outGctFile.write('NAME\tDescription\t%s\n' % '\t'.join(sIdL))
for geneName in geneNameL:
print geneName
trans = mygenome.transcript(
geneName, inRefFlatFileName,
'hg18') # consider only the longest transcript per gene
h = {}
for sId in sIdL:
h[sId] = 0.
for tokL in inSegFileMem:
(sId, chrNum, chrSta, chrEnd, numMarker, value) = tokL
if chrNum != trans.chrNum or value in ('NA', 'null', 'NULL'):
continue
overlap = trans.cdsOverlap((chrNum, int(chrSta), int(chrEnd)))
sIdL = list(set([tokL[0] for tokL in inSegFileMem]))
sIdL.sort()
#outGctFileName = '%s.gct' % mygp.stripPath(inSegFileName)[0]
#outGctFile = open(outGctFileName,'w')
outGctFile.write('#1.2\n')
outGctFile.write('%s\t%s\n' % (len(geneNameL),len(sIdL)))
outGctFile.write('NAME\tDescription\t%s\n' % '\t'.join(sIdL))
for geneName in geneNameL:
print geneName
trans = mygenome.transcript(geneName,inRefFlatFileName,assembly)
h = {}
for sId in sIdL:
h[sId] = 0.
for tokL in inSegFileMem:
(sId,chrNum,chrSta,chrEnd,numMarker,value) = tokL
if chrNum != trans.chrNum or value in ('NA','null','NULL'):
continue
overlap = trans.cdsOverlap((chrNum,int(chrSta),int(chrEnd)))
sIdL = list(set([tokL[0] for tokL in inSegFileMem]))
sIdL.sort()
#outGctFileName = '%s.gct' % mygp.stripPath(inSegFileName)[0]
#outGctFile = open(outGctFileName,'w')
outGctFile.write('#1.2\n')
outGctFile.write('%s\t%s\n' % (len(geneNameL), len(sIdL)))
outGctFile.write('NAME\tDescription\t%s\n' % '\t'.join(sIdL))
for geneName in geneNameL:
print geneName
trans = mygenome.transcript(geneName, inRefFlatFileName, assembly)
h = {}
for sId in sIdL:
h[sId] = 0.
for tokL in inSegFileMem:
(sId, chrNum, chrSta, chrEnd, numMarker, value) = tokL
if chrNum != trans.chrNum or value in ('NA', 'null', 'NULL'):
continue
overlap = trans.cdsOverlap((chrNum, int(chrSta), int(chrEnd)))
