def gene_annot(geneN_idx=0, inFileN='', outFileN='', have_header=True):
geneDB = mygenome.getGeneDB()
inFile = sys.stdin
if inFileN != '':
inFile = open(inFileN, 'r')
outFile = sys.stdout
if outFileN != '':
outFile = open(outFileN, 'w')
if have_header:
header = inFile.readline()[:-1]
outFile.write('%s\tgeneInfo\tcensus\tGO\tKEGG\tBiocarta\n' % header)
else:
last_pos = inFile.tell() # remember current position
header = inFile.readline().rstrip()
ncol = len(header.split('\t'))
headerL = map(lambda x: 'X%s' % (x + 1), range(ncol))
outFile.write('%s\tgeneInfo\tcensus\tGO\tKEGG\tBiocarta\n' %
'\t'.join(headerL))
inFile.seek(last_pos) # return to original position
#if have_header
for line in inFile:
tokL = line[:-1].split('\t')
geneName = tokL[geneN_idx].split(',')[0]
geneS = set()
geneH = {}
geneInfo = []
censusInfo = []
goInfoS = set()
keggInfoS = set()
biocInfoS = set()
gene = mygenome.gene(geneName, geneDB=geneDB)
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('biocarta')))
outFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % \
('\t'.join(tokL), ';'.join(geneInfo),';'.join(censusInfo), \
';'.join(map(str,goInfoS)), ';'.join(map(str,keggInfoS)),';'.join(map(str,biocInfoS))))
outFile.flush()
outFile.close()
inFile.close()
def gene_annot(inReportFileName, outReportFileName):
geneDB = mygenome.getGeneDB()
outReportFile = open(outReportFileName, 'w')
inFile = open(inReportFileName)
header = inFile.readline()[:-1]
outReportFile.write('%s\tgeneInfo\tcensus\tGO\tKEGG\tBiocarta\n' % header)
headerL = header.split('\t')
if 'geneN' in headerL:
geneN_idx = headerL.index('geneN')
if 'gene_symL' in headerL:
geneN_idx = headerL.index('gene_symL')
if 'SYMBOL' in headerL:
geneN_idx = headerL.index('SYMBOL')
for line in inFile:
tokL = line[:-1].split('\t')
# geneName = tokL[geneN_idx].split(',')[0]
geneName = tokL[geneN_idx].split(';')[0]
geneS = set()
geneH = {}
geneInfo = []
censusInfo = []
goInfoS = set()
keggInfoS = set()
biocInfoS = set()
gene = mygenome.gene(geneName, geneDB=geneDB)
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('biocarta')))
outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % \
('\t'.join(tokL), ';'.join(geneInfo),';'.join(censusInfo), \
';'.join(map(str,goInfoS)), ';'.join(map(str,keggInfoS)),';'.join(map(str,biocInfoS))))
def gene_annot(inReportFileName,outReportFileName):
geneDB = mygenome.getGeneDB()
outReportFile = open(outReportFileName,'w')
inFile = open(inReportFileName)
header = inFile.readline()[:-1]
outReportFile.write('%s\tgeneInfo\tcensus\tGO\tKEGG\tBiocarta\n' % header)
headerL = header.split('\t')
if 'geneN' in headerL:
geneN_idx = headerL.index('geneN')
if 'gene_symL' in headerL:
geneN_idx = headerL.index('gene_symL')
if 'SYMBOL' in headerL:
geneN_idx = headerL.index('SYMBOL')
for line in inFile:
tokL = line[:-1].split('\t')
# geneName = tokL[geneN_idx].split(',')[0]
geneName = tokL[geneN_idx].split(';')[0]
geneS = set()
geneH = {}
geneInfo = []
censusInfo = []
goInfoS = set()
keggInfoS = set()
biocInfoS = set()
gene = mygenome.gene(geneName,geneDB=geneDB)
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('biocarta')))
outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % \
('\t'.join(tokL), ';'.join(geneInfo),';'.join(censusInfo), \
';'.join(map(str,goInfoS)), ';'.join(map(str,keggInfoS)),';'.join(map(str,biocInfoS))))
def gene_annot(geneN_idx=0, inFileN="", outFileN="", have_header=True):
geneDB = mygenome.getGeneDB()
inFile = sys.stdin
if inFileN != "":
inFile = open(inFileN, "r")
outFile = sys.stdout
if outFileN != "":
outFile = open(outFileN, "w")
if have_header:
header = inFile.readline()[:-1]
outFile.write("%s\tgeneInfo\tcensus\tGO\tKEGG\tBiocarta\n" % header)
else:
last_pos = inFile.tell() # remember current position
header = inFile.readline().rstrip()
ncol = len(header.split("\t"))
headerL = map(lambda x: "X%s" % (x + 1), range(ncol))
outFile.write("%s\tgeneInfo\tcensus\tGO\tKEGG\tBiocarta\n" % "\t".join(headerL))
inFile.seek(last_pos) # return to original position
# if have_header
for line in inFile:
tokL = line[:-1].split("\t")
geneName = tokL[geneN_idx].split(",")[0]
geneS = set()
geneH = {}
geneInfo = []
censusInfo = []
goInfoS = set()
keggInfoS = set()
biocInfoS = set()
gene = mygenome.gene(geneName, geneDB=geneDB)
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("biocarta")))
outFile.write(
"%s\t%s\t%s\t%s\t%s\t%s\n"
% (
"\t".join(tokL),
";".join(geneInfo),
";".join(censusInfo),
";".join(map(str, goInfoS)),
";".join(map(str, keggInfoS)),
";".join(map(str, biocInfoS)),
)
)
outFile.flush()
outFile.close()
inFile.close()
def exonSkip_proc(inGsnapFileName, outGsnapFileName, outReportFileName, sampN):
geneNameH = mygenome.geneNameH()
geneSetH = mygenome.geneSetH()
geneInfoH = mygenome.geneInfoH(geneNameH, geneSetH)
refFlatH = mygenome.loadRefFlatByChr()
result = mygsnap.gsnapFile(inGsnapFileName, False)
juncHH = {}
for r in result:
match = r.matchL()[0]
if not '(transloc)' in r.pairRel:
raise Exception
if len(match.segL) != 2:
raise Exception
splice_type = re.search('splice_type:([^,\t]*)',
match.segL[0][3]).group(1)
direction = re.search('dir:([^,\t]*)', match.segL[0][3]).group(1)
offset = int(re.search('\.\.([0-9]*)', match.segL[0][1]).group(1))
transcript1 = re.search('label_[12]:([^,\t]*)', match.segL[0][3])
gene1 = set()
if transcript1:
transcript1 = tuple(
[x.split('.exon')[0] for x in transcript1.group(1).split('|')])
for t in transcript1:
g = mygenome.gene(t, geneNameH, geneSetH, geneInfoH)
if g.geneName:
gene1.add(g.geneName)
else:
transcript1 = ()
transcript2 = re.search('label_[12]:([^,\t]*)', match.segL[1][3])
gene2 = set()
if transcript2:
transcript2 = tuple(
[x.split('.exon')[0] for x in transcript2.group(1).split('|')])
for t in transcript2:
g = mygenome.gene(t, geneNameH, geneSetH, geneInfoH)
if g.geneName:
gene2.add(g.geneName)
else:
transcript2 = ()
s1 = match.segL[0][2]
s2 = match.segL[1][2]
bp1 = re.match('([+-])([^:]+):[0-9]+..([0-9]+)', s1)
bp2 = re.match('([+-])([^:]+):([0-9]+)..[0-9]+', s2)
if (bp1.group(1), direction) in (('+', 'sense'), ('-', 'antisense')):
trans_strand1 = '+'
elif (bp1.group(1), direction) in (('+', 'antisense'), ('-', 'sense')):
trans_strand1 = '-'
else:
raise Exception
if (bp2.group(1), direction) in (('+', 'sense'), ('-', 'antisense')):
trans_strand2 = '+'
elif (bp2.group(1), direction) in (('+', 'antisense'), ('-', 'sense')):
trans_strand2 = '-'
else:
raise Exception
bp_gene1 = mygenome.locus(
'%s:%s-%s%s' % (bp1.group(2), int(bp1.group(3)) - 1, bp1.group(3),
trans_strand1)).overlappingGeneL(
refFlatH=refFlatH, strand_sensitive=True)
bp_gene2 = mygenome.locus(
'%s:%s-%s%s' % (bp2.group(2), int(bp2.group(3)) - 1, bp2.group(3),
trans_strand2)).overlappingGeneL(
refFlatH=refFlatH, strand_sensitive=True)
if direction == 'sense':
key = (bp1.groups()[1:], bp2.groups()[1:])
transcript = (transcript1, transcript2)
gene = (tuple(gene1), tuple(gene2))
bp_gene = (bp_gene1, bp_gene2)
elif direction == 'antisense':
key = (bp2.groups()[1:], bp1.groups()[1:])
transcript = (transcript2, transcript1)
gene = (tuple(gene2), tuple(gene1))
bp_gene = (bp_gene2, bp_gene1)
else:
raise Exception
if key in juncHH:
juncHH[key]['match'].append(r)
juncHH[key]['seq'].append(r.seq())
juncHH[key]['reg'].append((direction, offset))
else:
juncHH[key] = {
'match': [r],
'splice_type': splice_type,
'seq': [r.seq()],
'reg': [(direction, offset)],
'transcript': transcript,
'gene': gene,
'bp_gene': bp_gene
}
juncKH = juncHH.items()
juncKH.sort(lambda x, y: cmp(len(set(y[1]['reg'])), len(set(x[1]['reg']))))
outGsnapFile = open(outGsnapFileName, 'w')
outReportFile = open(outReportFileName, 'w')
for (key, juncH) in juncKH:
if key[0][0] == key[1][0]:
type = 'intra'
else:
type = 'inter'
geneInfo1 = []
censusInfo1 = []
for geneName in juncH['gene'][0]:
gene = mygenome.gene(geneName, geneNameH, geneSetH, geneInfoH)
geneInfo1.append(
'%s:%s:%s' %
(geneName, gene.getAttr('desc'), gene.getAttr('summary')))
censusInfo1.append('%s:%s:%s:%s' %
(gene.getAttr('census_somatic'),
gene.getAttr('census_germline'),
gene.getAttr('census_mutType'),
gene.getAttr('census_translocPartners')))
geneInfo2 = []
censusInfo2 = []
for geneName in juncH['gene'][1]:
gene = mygenome.gene(geneName, geneNameH, geneSetH, geneInfoH)
geneInfo2.append(
'%s:%s:%s' %
(geneName, gene.getAttr('desc'), gene.getAttr('summary')))
censusInfo2.append('%s:%s:%s:%s' %
(gene.getAttr('census_somatic'),
gene.getAttr('census_germline'),
gene.getAttr('census_mutType'),
gene.getAttr('census_translocPartners')))
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\n' % \
(type, juncH['splice_type'], sampN, ':'.join(key[0]), ':'.join(key[1]), \
';'.join(juncH['transcript'][0]), ';'.join(juncH['transcript'][1]), ';'.join(juncH['gene'][0]), ';'.join(juncH['gene'][1]), ';'.join(geneInfo1), ';'.join(geneInfo2), \
';'.join(censusInfo1), ';'.join(censusInfo2), ','.join(juncH['bp_gene'][0]), ','.join(juncH['bp_gene'][1]), \
len(juncH['match']) ,len(set(juncH['seq'])), len(set(juncH['reg']))))
for m in juncH['match']:
outGsnapFile.write(m.rawText() + '\n')
def genCompositeModel(outTextFileName,outFaFileName,intronSize=100):
geneNameH = mygenome.geneNameH()
geneSetH = mygenome.geneSetH()
geneInfoH = mygenome.geneInfoH(geneNameH,geneSetH)
geneH = mygenome.loadKgByChr()
#geneH = mygenome.loadLincByChr(h=geneH)
outTextFile = open(outTextFileName, 'w')
outFaFile = open(outFaFileName, 'w')
for chrNum in range(1,23)+['X','Y','M']:
#for chrNum in [1]:
chrom = 'chr%s' % chrNum
geneH_byChr = filter(lambda x: mygenome.gene(x['geneId'],geneNameH,geneSetH,geneInfoH).geneName in mygenome.TK, geneH[chrom])
txnLocusL_combined = []
for strand in ['+','-']:
txnLocusL = [mygenome.locus('%s:%s-%s%s' % (chrom,h['txnSta'],h['txnEnd'],strand),h['geneId']) for h in filter(lambda x: x['strand']==strand, geneH_byChr)]
n_before = len(txnLocusL)
txnLocusL = mygenome.mergeLoci(txnLocusL)
n_after = len(txnLocusL)
#print chrom, strand, n_before, n_after
txnLocusL_combined += txnLocusL
txnLocusL_combined.sort(lambda x,y: cmp(x.chrEnd,y.chrEnd))
txnLocusL_combined.sort(lambda x,y: cmp(x.chrSta,y.chrSta))
for txnLoc in txnLocusL_combined:
exnLocusL = []
for h in filter(lambda x: x['geneId'] in txnLoc.id, geneH_byChr):
for (exnSta,exnEnd) in h['exnList']:
exnLocusL.append(mygenome.locus('%s:%s-%s%s' % (chrom, exnSta, exnEnd, h['strand'])))
exnLocusL.sort(lambda x,y: cmp(x.chrEnd,y.chrEnd))
exnLocusL.sort(lambda x,y: cmp(x.chrSta,y.chrSta))
exnLocusL = mygenome.mergeLoci(exnLocusL)
exnStaL = [str(exnLoc.chrSta) for exnLoc in exnLocusL]
exnEndL = [str(exnLoc.chrEnd) for exnLoc in exnLocusL]
outTextFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (txnLoc.id,txnLoc.chrom,txnLoc.strand,txnLoc.chrSta,txnLoc.chrEnd,len(exnLocusL),','.join(exnStaL),','.join(exnEndL)))
outFaFile.write('>%s|%s|%s|%s|%s\n' % (txnLoc.id,txnLoc.chrom,txnLoc.strand,txnLoc.chrSta,txnLoc.chrEnd))
for i in range(len(exnLocusL)):
exnLocCopy = copy.deepcopy(exnLocusL[i])
exnLocCopy.strand = '+'
if i > 0:
exnLocCopy.chrSta -= min(intronSize, int((exnLocusL[i].chrSta - exnLocusL[i-1].chrEnd)/2))
if i < len(exnLocusL)-1:
exnLocCopy.chrEnd += min(intronSize, int((exnLocusL[i+1].chrSta - exnLocusL[i].chrEnd)/2))
outFaFile.write(exnLocCopy.nibFrag())
outFaFile.write('\n')
outTextFile.close()
outFaFile.close()
def gsnap_process_junction(inGsnapFileName,outGsnapFileName,outReportFileName,sampN):
geneNameH = mygenome.geneNameH()
geneSetH = mygenome.geneSetH()
geneInfoH = mygenome.geneInfoH(geneNameH,geneSetH)
refFlatH = mygenome.loadRefFlatByChr()
result = mygsnap.gsnapFile(inGsnapFileName,False)
juncHH = {}
for r in result:
match = r.matchL()[0]
if not '(transloc)' in r.pairRel:
raise Exception
if len(match.segL) != 2:
raise Exception
splice_type = re.search('splice_type:([^,\t]*)', match.segL[0][3]).group(1)
direction = re.search('dir:([^,\t]*)', match.segL[0][3]).group(1)
offset = int(re.search('\.\.([0-9]*)', match.segL[0][1]).group(1))
rm = re.search('label_[12]:([^,\t]*)', match.segL[0][3])
gene1 = set()
if rm:
trans_exon1 = rm.group(1).split('|')
for t in trans_exon1:
g = mygenome.gene(t.split('.exon')[0],geneNameH,geneSetH,geneInfoH)
if g.geneName:
gene1.add(g.geneName)
else:
trans_exon1 = ()
rm = re.search('label_[12]:([^,\t]*)', match.segL[0][3])
gene2 = set()
if rm:
trans_exon2 = rm.group(1).split('|')
for t in trans_exon2:
g = mygenome.gene(t.split('.exon')[0],geneNameH,geneSetH,geneInfoH)
if g.geneName:
gene2.add(g.geneName)
else:
trans_exon2 = ()
s1 = match.segL[0][2]
s2 = match.segL[1][2]
bp1 = re.match('([+-])([^:]+):[0-9]+..([0-9]+)',s1)
bp2 = re.match('([+-])([^:]+):([0-9]+)..[0-9]+',s2)
if (bp1.group(1),direction) in (('+','sense'),('-','antisense')):
trans_strand1 = '+'
elif (bp1.group(1),direction) in (('+','antisense'),('-','sense')):
trans_strand1 = '-'
else:
raise Exception
if (bp2.group(1),direction) in (('+','sense'),('-','antisense')):
trans_strand2 = '+'
elif (bp2.group(1),direction) in (('+','antisense'),('-','sense')):
trans_strand2 = '-'
else:
raise Exception
locus1 = mygenome.locus('%s:%s-%s%s' % (bp1.group(2),int(bp1.group(3))-1,bp1.group(3),trans_strand1))
bp_gene1 = list(set(locus1.overlappingGeneL(refFlatH=refFlatH,strand_sensitive=True)).difference(gene1))
locus2 = mygenome.locus('%s:%s-%s%s' % (bp2.group(2),int(bp2.group(3))-2,bp2.group(3),trans_strand2))
bp_gene2 = list(set(locus2.overlappingGeneL(refFlatH=refFlatH,strand_sensitive=True)).difference(gene2))
if direction=='sense':
key = (bp1.groups()[1:],bp2.groups()[1:])
trans_exon = (trans_exon1,trans_exon2)
gene = (list(gene1),list(gene2))
bp_gene = (bp_gene1,bp_gene2)
elif direction=='antisense':
key = (bp2.groups()[1:],bp1.groups()[1:])
trans_exon = (trans_exon2,trans_exon1)
gene = (list(gene2),list(gene1))
bp_gene = (bp_gene2,bp_gene1)
else:
raise Exception
if key in juncHH:
juncHH[key]['match'].append(r)
juncHH[key]['seq'].append(r.seq())
juncHH[key]['reg'].append((direction,offset))
else:
juncHH[key] = {'match':[r], 'splice_type':splice_type, 'seq':[r.seq()], 'reg':[(direction,offset)], 'trans_exon':trans_exon, 'gene':gene, 'bp_gene':bp_gene}
juncKH = juncHH.items()
juncKH.sort(lambda x,y: cmp(len(set(y[1]['reg'])),len(set(x[1]['reg']))))
outGsnapFile = open(outGsnapFileName,'w')
outReportFile = open(outReportFileName,'w')
for (key, juncH) in juncKH:
if key[0][0] == key[1][0]:
type = 'intra'
else:
type = 'inter'
geneInfo1 = []
censusInfo1 = []
for geneName in juncH['gene'][0]+juncH['bp_gene'][0]:
gene = mygenome.gene(geneName,geneNameH,geneSetH,geneInfoH)
geneInfo1.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
censusInfo1.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))
geneInfo2 = []
censusInfo2 = []
for geneName in juncH['gene'][1]+juncH['bp_gene'][1]:
gene = mygenome.gene(geneName,geneNameH,geneSetH,geneInfoH)
geneInfo2.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
censusInfo2.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))
outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s;%s\t%s;%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
(type, juncH['splice_type'], sampN, ':'.join(key[0]), ':'.join(key[1]), \
','.join(juncH['trans_exon'][0]), ','.join(juncH['trans_exon'][1]), \
','.join(juncH['gene'][0]), ','.join(juncH['bp_gene'][0]), ','.join(juncH['gene'][1]), ','.join(juncH['bp_gene'][1]), \
';'.join(geneInfo1), ';'.join(geneInfo2), ';'.join(censusInfo1), ';'.join(censusInfo2), \
len(juncH['match']) ,len(set(juncH['seq'])), len(set(juncH['reg']))))
for m in juncH['match']:
outGsnapFile.write(m.rawText()+'\n')
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 gsnap_process_junction(inReportFileName,outReportFileName):
geneNameH = mygenome.geneNameH()
geneSetH = mygenome.geneSetH()
geneInfoH = mygenome.geneInfoH(geneNameH,geneSetH)
outReportFile = open(outReportFileName,'w')
for line in open(inReportFileName):
(spliceType,sampN,bp1,bp2,t1,t2,nmatch,nseq,nreg) = line[:-1].split('\t')
gene1 = set()
if t1:
transcript1 = tuple(t1.split(';'))
for t in transcript1:
g = mygenome.gene(t,geneNameH,geneSetH,geneInfoH)
if g.geneName:
gene1.add(g.geneName)
else:
gene1 = ()
gene2 = set()
if t2:
transcript2 = tuple(t2.split(';'))
for t in transcript2:
g = mygenome.gene(t,geneNameH,geneSetH,geneInfoH)
if g.geneName:
gene2.add(g.geneName)
else:
gene2 = ()
bp_gene1 = set()
# transcript1 = tuple([x for x in bp1.split('|') if "uc" in x])
for t in tuple([x for x in bp1.split('|') if "uc" in x]):
g = mygenome.gene(t,geneNameH,geneSetH,geneInfoH)
if g.geneName:
bp_gene1.add(g.geneName)
bp_gene2 = set()
# transcript2 = tuple([x for x in bp2.split('|') if "uc" in x])
for t in tuple([x for x in bp2.split('|') if "uc" in x]):
g = mygenome.gene(t,geneNameH,geneSetH,geneInfoH)
if g.geneName:
bp_gene2.add(g.geneName)
# ch1 = tuple([x for x in id1.split('|') if not "uc" in x])
# ch2 = tuple([x for x in id2.split('|') if not "uc" in x])
if tuple([x for x in bp1.split('|') if "chr" in x])[0] == tuple([x for x in bp2.split('|') if "chr" in x])[0]:
type = 'intra'
else:
type = 'inter'
geneInfo1 = []
censusInfo1 = []
for geneName in gene1:
gene = mygenome.gene(geneName,geneNameH,geneSetH,geneInfoH)
geneInfo1.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
censusInfo1.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))
geneInfo2 = []
censusInfo2 = []
for geneName in gene2:
gene = mygenome.gene(geneName,geneNameH,geneSetH,geneInfoH)
geneInfo2.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
censusInfo2.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))
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\n' % \
(type, spliceType, sampN, bp1, bp2, \
t1, t2, ';'.join(gene1), ';'.join(gene2), ';'.join(geneInfo1), ';'.join(geneInfo2), \
';'.join(censusInfo1), ';'.join(censusInfo2), ','.join(bp_gene1), ','.join(bp_gene2), \
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))
def gsnap_process_junction(inReportFileName, outReportFileName):
geneNameH = mygenome.geneNameH()
geneSetH = mygenome.geneSetH()
geneInfoH = mygenome.geneInfoH(geneNameH, geneSetH)
outReportFile = open(outReportFileName, 'w')
for line in open(inReportFileName):
(spliceType, sampN, bp1, bp2, t1, t2, nmatch, nseq,
nreg) = line[:-1].split('\t')
gene1 = set()
if t1:
transcript1 = tuple(t1.split(';'))
for t in transcript1:
g = mygenome.gene(t, geneNameH, geneSetH, geneInfoH)
if g.geneName:
gene1.add(g.geneName)
else:
gene1 = ()
gene2 = set()
if t2:
transcript2 = tuple(t2.split(';'))
for t in transcript2:
g = mygenome.gene(t, geneNameH, geneSetH, geneInfoH)
if g.geneName:
gene2.add(g.geneName)
else:
gene2 = ()
bp_gene1 = set()
# transcript1 = tuple([x for x in bp1.split('|') if "uc" in x])
for t in tuple([x for x in bp1.split('|') if "uc" in x]):
g = mygenome.gene(t, geneNameH, geneSetH, geneInfoH)
if g.geneName:
bp_gene1.add(g.geneName)
bp_gene2 = set()
# transcript2 = tuple([x for x in bp2.split('|') if "uc" in x])
for t in tuple([x for x in bp2.split('|') if "uc" in x]):
g = mygenome.gene(t, geneNameH, geneSetH, geneInfoH)
if g.geneName:
bp_gene2.add(g.geneName)
# ch1 = tuple([x for x in id1.split('|') if not "uc" in x])
# ch2 = tuple([x for x in id2.split('|') if not "uc" in x])
if tuple([x for x in bp1.split('|') if "chr" in x
])[0] == tuple([x for x in bp2.split('|') if "chr" in x])[0]:
type = 'intra'
else:
type = 'inter'
geneInfo1 = []
censusInfo1 = []
for geneName in gene1:
gene = mygenome.gene(geneName, geneNameH, geneSetH, geneInfoH)
geneInfo1.append(
'%s:%s:%s' %
(geneName, gene.getAttr('desc'), gene.getAttr('summary')))
censusInfo1.append('%s:%s:%s:%s' %
(gene.getAttr('census_somatic'),
gene.getAttr('census_germline'),
gene.getAttr('census_mutType'),
gene.getAttr('census_translocPartners')))
geneInfo2 = []
censusInfo2 = []
for geneName in gene2:
gene = mygenome.gene(geneName, geneNameH, geneSetH, geneInfoH)
geneInfo2.append(
'%s:%s:%s' %
(geneName, gene.getAttr('desc'), gene.getAttr('summary')))
censusInfo2.append('%s:%s:%s:%s' %
(gene.getAttr('census_somatic'),
gene.getAttr('census_germline'),
gene.getAttr('census_mutType'),
gene.getAttr('census_translocPartners')))
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\n' % \
(type, spliceType, sampN, bp1, bp2, \
t1, t2, ';'.join(gene1), ';'.join(gene2), ';'.join(geneInfo1), ';'.join(geneInfo2), \
';'.join(censusInfo1), ';'.join(censusInfo2), ','.join(bp_gene1), ','.join(bp_gene2), \
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))