def exonSkip_proc_annot(inReportFileName,outReportFileName,inCnaGctFileName=None):
geneDB = mygenome.getGeneDB()
frameInfoH = mygenome.getFrameInfoH()
if inCnaGctFileName:
cnaDB = mygenome.tcgaCnaDB(inCnaGctFileName)
else:
cnaDB = None
outReportFile = open(outReportFileName,'w')
for line in open(inReportFileName):
(sampN,bp1,bp2,t1,t2,nmatch,nseq,nreg) = line[:-1].split('\t')
if inCnaGctFileName:
indivId = re.match('.*(TCGA-[0-9]{2}-[0-9]{4}).*',sampN).group(1)
geneS = set()
geneH = {}
for tL in (t1,t2):
for t in tL.split(','):
ro = re.match('(.*)\.exon([0-9]*)/[0-9]*',t)
t = ro.group(1)
e = int(ro.group(2))
mybasic.addHash(geneH,t,e)
g = mygenome.gene(t,geneDB=geneDB)
if g.geneName:
geneS.add(g.geneName)
frameL = []
for transId in geneH:
exnList = geneH[transId]
if len(exnList) != 2:
continue
#exnList.sort()
cons = mygenome.frameCons(transId,exnList[0], transId,exnList[1],frameInfoH)
if cons:
frameL.append('%s:%s' % (transId,cons))
else:
continue
cnaInfo = []
geneInfo = []
censusInfo = []
goInfoS = set()
keggInfoS = set()
biocInfoS = set()
for geneName in geneS:
gene = mygenome.gene(geneName,geneDB=geneDB)
if cnaDB:
cnaInfo.append('%s:%s' % (geneName,cnaDB.query(indivId,geneName)))
geneInfo.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
censusInfo.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))
goInfoS = goInfoS.union(set(gene.getAttr('go')))
keggInfoS = keggInfoS.union(set(gene.getAttr('kegg')))
biocInfoS = biocInfoS.union(set(gene.getAttr('bioc')))
outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
(sampN, bp1,bp2, t1,t2, ','.join(frameL), ';'.join(geneS), ','.join(cnaInfo),';'.join(geneInfo),';'.join(censusInfo), \
';'.join(map(str,goInfoS)), ';'.join(map(str,keggInfoS)),';'.join(map(str,biocInfoS)),nmatch,nseq,nreg))
def fusion_proc_annot(inReportFileName,outReportFileName,inCnaGctFileName=None):
geneDB = mygenome.getGeneDB()
frameInfoH = mygenome.getFrameInfoH()
refFlatH = mygenome.loadRefFlatByChr()
if inCnaGctFileName:
cnaDB = mygenome.tcgaCnaDB(inCnaGctFileName)
else:
cnaDB = None
outReportFile = open(outReportFileName,'w')
for line in open(inReportFileName):
(splice_type,sampN,bp1,bp2,teStr1,teStr2,nmatch,nseq,nreg) = line[:-1].split('\t')
if inCnaGctFileName:
indivId = re.match('.*(TCGA-[0-9]{2}-[0-9]{4}).*',sampN).group(1)
geneStatL = []
for (bp,teStr) in ((bp1,teStr1),(bp2,teStr2)):
geneS = set()
teL = []
for te in teStr.split(','):
rm = re.match('(.*)\.exon([0-9]*)/[0-9]*',te)
if rm:
t = rm.group(1)
e = int(rm.group(2))
g = mygenome.gene(t,geneDB=geneDB)
if g.geneName:
geneS.add(g.geneName)
teL.append((t,e))
rm = re.match('([+-])(chr[^:]*):([0-9]*)',bp)
bp_geneS = set(mygenome.locus('%s:%s-%s%s' % (rm.group(2),int(rm.group(3))-1,rm.group(3),rm.group(1))).overlappingGeneL(refFlatH=refFlatH,strand_sensitive=True))
bp_geneS = bp_geneS.difference(geneS)
cnaInfo = []
geneInfo = []
censusInfo = []
goInfoS = set()
keggInfoS = set()
biocartaInfoS = set()
for geneName in list(geneS) + list(bp_geneS):
gene = mygenome.gene(geneName,geneDB=geneDB)
if cnaDB:
cnaInfo.append('%s:%s' % (geneName,cnaDB.query(indivId,geneName)))
geneInfo.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
censusInfo.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))
goInfoS = goInfoS.union(set(gene.getAttr('go')))
keggInfoS = keggInfoS.union(set(gene.getAttr('kegg')))
biocartaInfoS = biocartaInfoS.union(set(gene.getAttr('biocarta')))
geneStatL.append((bp1.split(':')[0],bp,teStr,teL,geneS,bp_geneS,cnaInfo,geneInfo,censusInfo,goInfoS,keggInfoS,biocartaInfoS))
(chrom1,bp1,teStr1,teL1,geneS1,bp_geneS1,cnaInfo1,geneInfo1,censusInfo1,goInfoS1,keggInfoS1,biocartaInfoS1) = geneStatL[0]
(chrom2,bp2,teStr2,teL2,geneS2,bp_geneS2,cnaInfo2,geneInfo2,censusInfo2,goInfoS2,keggInfoS2,biocartaInfoS2) = geneStatL[1]
if chrom1 == chrom2:
type = 'intra'
else:
type = 'inter'
frameL = []
for (t1,e1) in teL1:
for (t2,e2) in teL2:
cons = mygenome.frameCons(t1,e1, t2,e2, frameInfoH)
if cons=='Y':
frameL.append('%s.%s-%s.%s:%s' % (t1,e1,t2,e2,cons))
outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
(sampN, splice_type, type, bp1,bp2, teStr1,teStr2, ','.join(frameL), ','.join(cnaInfo1), ','.join(cnaInfo2), \
'%s;%s' % (','.join(geneS1),','.join(bp_geneS1)), ';'.join(geneInfo1), ';'.join(censusInfo1), \
';'.join(map(str,goInfoS1)), ';'.join(map(str,keggInfoS1)), ';'.join(map(str,biocartaInfoS1)),
'%s;%s' % (','.join(geneS2),','.join(bp_geneS2)), ';'.join(geneInfo2), ';'.join(censusInfo2), \
';'.join(map(str,goInfoS2)), ';'.join(map(str,keggInfoS2)), ';'.join(map(str,biocartaInfoS2)),
nmatch,nseq,nreg))
def exonSkip_proc_annot(inReportFileName,
outReportFileName,
inCnaGctFileName=None):
geneDB = mygenome.getGeneDB()
frameInfoH = mygenome.getFrameInfoH()
if inCnaGctFileName:
cnaDB = mygenome.tcgaCnaDB(inCnaGctFileName)
else:
cnaDB = None
outReportFile = open(outReportFileName, 'w')
for line in open(inReportFileName):
(sampN, bp1, bp2, t1, t2, nmatch, nseq, nreg) = line[:-1].split('\t')
if inCnaGctFileName:
indivId = re.match('.*(TCGA-[0-9]{2}-[0-9]{4}).*', sampN).group(1)
geneS = set()
geneH = {}
for tL in (t1, t2):
for t in tL.split(','):
ro = re.match('(.*)\.exon([0-9]*)/[0-9]*', t)
t = ro.group(1)
e = int(ro.group(2))
mybasic.addHash(geneH, t, e)
g = mygenome.gene(t, geneDB=geneDB)
if g.geneName:
geneS.add(g.geneName)
frameL = []
for transId in geneH:
exnList = geneH[transId]
if len(exnList) != 2:
continue
#exnList.sort()
cons = mygenome.frameCons(transId, exnList[0], transId, exnList[1],
frameInfoH)
if cons:
frameL.append('%s:%s' % (transId, cons))
else:
continue
cnaInfo = []
geneInfo = []
censusInfo = []
goInfoS = set()
keggInfoS = set()
biocInfoS = set()
for geneName in geneS:
gene = mygenome.gene(geneName, geneDB=geneDB)
if cnaDB:
cnaInfo.append('%s:%s' %
(geneName, cnaDB.query(indivId, geneName)))
geneInfo.append(
'%s:%s:%s' %
(geneName, gene.getAttr('desc'), gene.getAttr('summary')))
censusInfo.append('%s:%s:%s:%s' %
(gene.getAttr('census_somatic'),
gene.getAttr('census_germline'),
gene.getAttr('census_mutType'),
gene.getAttr('census_translocPartners')))
goInfoS = goInfoS.union(set(gene.getAttr('go')))
keggInfoS = keggInfoS.union(set(gene.getAttr('kegg')))
biocInfoS = biocInfoS.union(set(gene.getAttr('bioc')))
outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
(sampN, bp1,bp2, t1,t2, ','.join(frameL), ';'.join(geneS), ','.join(cnaInfo),';'.join(geneInfo),';'.join(censusInfo), \
';'.join(map(str,goInfoS)), ';'.join(map(str,keggInfoS)),';'.join(map(str,biocInfoS)),nmatch,nseq,nreg))
def fusion_proc_annot(inReportFileName,
outReportFileName,
inCnaGctFileName=None):
geneDB = mygenome.getGeneDB()
frameInfoH = mygenome.getFrameInfoH()
refFlatH = mygenome.loadRefFlatByChr()
if inCnaGctFileName:
cnaDB = mygenome.tcgaCnaDB(inCnaGctFileName)
else:
cnaDB = None
outReportFile = open(outReportFileName, 'w')
for line in open(inReportFileName):
(splice_type, sampN, bp1, bp2, teStr1, teStr2, nmatch, nseq,
nreg) = line[:-1].split('\t')
if inCnaGctFileName:
indivId = re.match('.*(TCGA-[0-9]{2}-[0-9]{4}).*', sampN).group(1)
geneStatL = []
for (bp, teStr) in ((bp1, teStr1), (bp2, teStr2)):
geneS = set()
teL = []
for te in teStr.split(','):
rm = re.match('(.*)\.exon([0-9]*)/[0-9]*', te)
if rm:
t = rm.group(1)
e = int(rm.group(2))
g = mygenome.gene(t, geneDB=geneDB)
if g.geneName:
geneS.add(g.geneName)
teL.append((t, e))
rm = re.match('([+-])(chr[^:]*):([0-9]*)', bp)
bp_geneS = set(
mygenome.locus('%s:%s-%s%s' %
(rm.group(2), int(rm.group(3)) - 1, rm.group(3),
rm.group(1))).overlappingGeneL(
refFlatH=refFlatH, strand_sensitive=True))
bp_geneS = bp_geneS.difference(geneS)
cnaInfo = []
geneInfo = []
censusInfo = []
goInfoS = set()
keggInfoS = set()
biocartaInfoS = set()
for geneName in list(geneS) + list(bp_geneS):
gene = mygenome.gene(geneName, geneDB=geneDB)
if cnaDB:
cnaInfo.append('%s:%s' %
(geneName, cnaDB.query(indivId, geneName)))
geneInfo.append(
'%s:%s:%s' %
(geneName, gene.getAttr('desc'), gene.getAttr('summary')))
censusInfo.append('%s:%s:%s:%s' %
(gene.getAttr('census_somatic'),
gene.getAttr('census_germline'),
gene.getAttr('census_mutType'),
gene.getAttr('census_translocPartners')))
goInfoS = goInfoS.union(set(gene.getAttr('go')))
keggInfoS = keggInfoS.union(set(gene.getAttr('kegg')))
biocartaInfoS = biocartaInfoS.union(
set(gene.getAttr('biocarta')))
geneStatL.append(
(bp1.split(':')[0], bp, teStr, teL, geneS, bp_geneS, cnaInfo,
geneInfo, censusInfo, goInfoS, keggInfoS, biocartaInfoS))
(chrom1, bp1, teStr1, teL1, geneS1, bp_geneS1, cnaInfo1, geneInfo1,
censusInfo1, goInfoS1, keggInfoS1, biocartaInfoS1) = geneStatL[0]
(chrom2, bp2, teStr2, teL2, geneS2, bp_geneS2, cnaInfo2, geneInfo2,
censusInfo2, goInfoS2, keggInfoS2, biocartaInfoS2) = geneStatL[1]
if chrom1 == chrom2:
type = 'intra'
else:
type = 'inter'
frameL = []
for (t1, e1) in teL1:
for (t2, e2) in teL2:
cons = mygenome.frameCons(t1, e1, t2, e2, frameInfoH)
if cons == 'Y':
frameL.append('%s.%s-%s.%s:%s' % (t1, e1, t2, e2, cons))
outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
(sampN, splice_type, type, bp1,bp2, teStr1,teStr2, ','.join(frameL), ','.join(cnaInfo1), ','.join(cnaInfo2), \
'%s;%s' % (','.join(geneS1),','.join(bp_geneS1)), ';'.join(geneInfo1), ';'.join(censusInfo1), \
';'.join(map(str,goInfoS1)), ';'.join(map(str,keggInfoS1)), ';'.join(map(str,biocartaInfoS1)),
'%s;%s' % (','.join(geneS2),','.join(bp_geneS2)), ';'.join(geneInfo2), ';'.join(censusInfo2), \
';'.join(map(str,goInfoS2)), ';'.join(map(str,keggInfoS2)), ';'.join(map(str,biocartaInfoS2)),
nmatch,nseq,nreg))