def parse(exon1,exon2):
h = {}
for t in exon1.split(','):
rm = re.match('(.+)\.exon(.+)\/(.+)',t)
h[(rm.group(1),int(rm.group(3)))] = [int(rm.group(2))]
for t in exon2.split(','):
rm = re.match('(.+)\.exon(.+)\/(.+)',t)
if (rm.group(1),int(rm.group(3))) in h:
h[(rm.group(1),int(rm.group(3)))].append(int(rm.group(2)))
h2 = {}
for t in h:
if len(h[t]) == 2:
mybasic.addHash(h2,tuple(h[t]),t)
h2_items = h2.items()
h2_items.sort(lambda x,y: cmp(len(y[1]),len(x[1])))
return ','.join(['%s-%s' % (eS+1,eE-1) for ((eS,eE),l) in h2_items])
def geneInfoH(geneNameH, geneSetH, refSeqSummaryFileName='/Z/Sequence/ucsc_hg19/annot/refSeqSummary.txt', hugoFileName='/Z/Sequence/geneinfo/hugo.txt', \
censusFileName='/Z/Sequence/geneinfo/cancer_gene_census.txt', biocartaFileName='/Z/Sequence/geneinfo/BIOCARTA.gmt', \
goFileName='/Z/Sequence/geneinfo/hugo.txt', keggFileName='/Z/Sequence/geneinfo/hugo.txt'):
geneInfoH = {}
for line in open(refSeqSummaryFileName):
(refSeqId,status,summary) = line[:-1].split('\t')
if refSeqId in geneNameH:
geneName = geneNameH[refSeqId]
if geneName not in geneInfoH:
geneInfoH[geneName] = {}
geneInfoH[geneName]['summary'] = summary
for line in open(hugoFileName):
(geneName,desc,aliases,geneCardName,refSeqIds) = line[:-1].split('\t')
if geneName not in geneInfoH:
geneInfoH[geneName] = {}
geneInfoH[geneName]['desc'] = desc
geneInfoH[geneName]['aliases'] = aliases
geneInfoH[geneName]['refSeqIds'] = refSeqIds
for line in open(censusFileName):
tokL = line[:-1].split('\t')
(geneName,desc,somatic,germline,mutType,translocPartners) = (tokL[0],tokL[1],tokL[7],tokL[8],tokL[12],tokL[13])
if geneName == 'Symbol':
continue
if geneName not in geneInfoH:
geneInfoH[geneName] = {'desc':desc}
geneInfoH[geneName]['census_somatic'] = somatic
geneInfoH[geneName]['census_germline'] = germline
geneInfoH[geneName]['census_mutType'] = mutType
geneInfoH[geneName]['census_translocPartners'] = translocPartners
for geneSetDB in geneSetH.keys():
for (geneSetName,(geneSetDesc,geneNameL)) in geneSetH[geneSetDB].iteritems():
for geneName in geneNameL:
if geneName in geneInfoH:
mybasic.addHash(geneInfoH[geneName],geneSetDB,(geneSetName,geneSetDesc))
else:
geneInfoH[geneName] = {geneSetDB:[(geneSetName,geneSetDesc)]}
return geneInfoH
def main(dirPath):
fileNameL = filter(lambda x: re.match('.*TCGA-..-....-0..*\.bam', x),
os.listdir(dirPath)) # normal sample, bam
fileNameTokL = map(
lambda x: re.match('.*(TCGA-..-....)-...-..([DW]).*\.bam', x),
fileNameL)
h = {}
for rm in fileNameTokL:
sN = rm.group(1)
type = rm.group(2)
if 'SOLiD' in rm.group(0):
type += '-SD'
elif 'IlluminaGA' in rm.group(0):
type += '-GA'
mybasic.addHash(h, sN, type)
for (sN, typeL) in h.iteritems():
typeL = list(set(typeL))
typeL.sort()
sys.stdout.write('%s\tXSeq_%s\n' % (sN, ','.join(typeL)))
def parse(exon1, exon2):
h = {}
for t in exon1.split(','):
rm = re.match('(.+)\.exon(.+)\/(.+)', t)
h[(rm.group(1), int(rm.group(3)))] = [int(rm.group(2))]
for t in exon2.split(','):
rm = re.match('(.+)\.exon(.+)\/(.+)', t)
if (rm.group(1), int(rm.group(3))) in h:
h[(rm.group(1), int(rm.group(3)))].append(int(rm.group(2)))
h2 = {}
for t in h:
if len(h[t]) == 2:
mybasic.addHash(h2, tuple(h[t]), t)
h2_items = h2.items()
h2_items.sort(lambda x, y: cmp(len(y[1]), len(x[1])))
return ','.join(['%s-%s' % (eS + 1, eE - 1) for ((eS, eE), l) in h2_items])
def loadKgByChr(dataFileName='/Z/Sequence/ucsc_hg19/annot/knownGene.txt',h={}):
for line in open(dataFileName):
r = processKgLine(line)
mybasic.addHash(h, r['chrom'], r)
return h
def loadLincByChr(dataFileName='/Z/Sequence/ucsc_hg19/annot/lincRNAsTranscripts.txt',h={}):
for line in open(dataFileName):
r = processLincLine(line)
mybasic.addHash(h, r['chrom'], r)
return h
def loadRefFlatByGene(refFlatFileName):
h = {}
for line in open(refFlatFileName):
r = processRefFlatLine(line)
mybasic.addHash(h, r['geneName'], r)
return h
def process_bp(inGsnapFileName):
result = mygsnap.gsnapFile(inGsnapFileName, False)
#outBpFile = open(outBpFileName, 'w')
seqH = {}
for r in result:
match = r.matchL()[0]
if not '(transloc)' in r.pairRel:
raise Exception
if len(match.segL) != 2:
raise Exception
s1 = match.segL[0][2]
s2 = match.segL[1][2]
direction = re.search('dir:([^,\t]*)', match.segL[0][3]).group(1)
bp1 = re.match('[+-]([^:]+):[0-9]+..([0-9]+)', s1).groups()
bp2 = re.match('[+-]([^:]+):([0-9]+)..[0-9]+', s2).groups()
# if bp1[0] == bp2[0]:
# continue
if direction == 'sense':
seq = r.seq()
offset = int(match.segL[0][1].split('..')[1])
bp12 = (bp1, bp2)
else:
seq = mybasic.rc(r.seq(), 'DNA')
offset = len(seq) - int(match.segL[0][1].split('..')[1])
bp12 = (bp2, bp1)
mybasic.addHash(seqH, bp12, (offset, seq))
seqL = seqH.items()
seqL.sort(lambda x, y: cmp(len(y[1]), len(x[1])))
for ((bp1, bp2), vL) in seqL:
vL.sort(lambda x, y: cmp(y[0], x[0]))
maxOffset = vL[0][0]
print '\n', bp1, bp2, len(vL), '\n'
for (offset, seq) in vL:
print '%s%s %s' % (' ' * (maxOffset - offset), seq[:offset],
seq[offset:])
def process_bp(inGsnapFileName, outBpFileName):
result = mygsnap.gsnapFile(inGsnapFileName, False)
outBpFile = open(outBpFileName, 'w')
seqH = {}
for r in result:
match = r.matchL()[0]
if not '(transloc)' in r.pairRel:
raise Exception
if len(match.segL) != 2:
raise Exception
s1 = match.segL[0][2]
s2 = match.segL[1][2]
if s1[0] != s2[0]:
raise Exception
strand = s1[0]
s1T = re.match('[+-]([^:]+):[0-9]+..([0-9]+)', s1).groups()
s2T = re.match('[+-]([^:]+):([0-9]+)..[0-9]+', s2).groups()
if strand == '+':
seq = r.seq()
offset = int(match.segL[0][1].split('..')[1])
junction = (s1T, s2T)
else:
seq = mybasic.rc(r.seq(), 'DNA')
offset = len(seq) - int(match.segL[0][1].split('..')[1])
junction = (s2T, s1T)
mybasic.addHash(seqH, junction, (offset, seq))
for ((j1, j2), vL) in seqH.items():
vL.sort(lambda x, y: cmp(x[0], y[0]))
vL_mod = []
for (offset, seq) in vL:
offset = blockSize - offset + 1
vL_mod.append('%s:%s' % (offset, seq))
outBpFile.write('%s:%s-%s,%s:%s-%s,%s\n' %
(j1[0].split('_')[0], int(j1[1]) - blockSize, j1[1],
j1[0].split('_')[0], j1[1], int(j1[1]) + blockSize,
'|'.join(vL_mod)))
def loadRefFlatByChr(refFlatFileName='/data1/Sequence/ucsc_hg19/annot/refFlat_splice_EGFR.txt'):
h = {}
for line in open(refFlatFileName):
r = mygenome.processRefFlatLine(line)
mybasic.addHash(h, r['chrom'], r)
return h
def process_bp(inGsnapFileName,outBpFileName):
result = mygsnap.gsnapFile(inGsnapFileName,False)
outBpFile = open(outBpFileName, 'w')
seqH = {}
for r in result:
match = r.matchL()[0]
if not '(transloc)' in r.pairRel:
raise Exception
if len(match.segL) != 2:
raise Exception
s1 = match.segL[0][2]
s2 = match.segL[1][2]
if s1[0] != s2[0]:
raise Exception
strand = s1[0]
s1T = re.match('[+-]([^:]+):[0-9]+..([0-9]+)',s1).groups()
s2T = re.match('[+-]([^:]+):([0-9]+)..[0-9]+',s2).groups()
if strand == '+':
seq = r.seq()
offset = int(match.segL[0][1].split('..')[1])
junction = (s1T, s2T)
else:
seq = mybasic.rc(r.seq(),'DNA')
offset = len(seq)-int(match.segL[0][1].split('..')[1])
junction = (s2T, s1T)
mybasic.addHash(seqH,junction,(offset,seq))
for ((k1,k2), v) in seqH.items():
v.sort(lambda x,y: cmp(y[0],x[0]))
k1T = re.match()
k2T = re.match()
k1_pos =
k2_pos =
k1_seq =
k2_seq =
outBpFile.write('%s,%s,%s\n' % (':'.join(k1),':'.join(k2),'|'.join(['%s:%s' % (offset,seq) for (offset,seq) in v])))
def process_bp(inGsnapFileName):
result = mygsnap.gsnapFile(inGsnapFileName,False)
#outBpFile = open(outBpFileName, 'w')
seqH = {}
for r in result:
match = r.matchL()[0]
if not '(transloc)' in r.pairRel:
raise Exception
if len(match.segL) != 2:
raise Exception
s1 = match.segL[0][2]
s2 = match.segL[1][2]
direction = re.search('dir:([^,\t]*)', match.segL[0][3]).group(1)
bp1 = re.match('[+-]([^:]+):[0-9]+..([0-9]+)',s1).groups()
bp2 = re.match('[+-]([^:]+):([0-9]+)..[0-9]+',s2).groups()
# if bp1[0] == bp2[0]:
# continue
if direction == 'sense':
seq = r.seq()
offset = int(match.segL[0][1].split('..')[1])
bp12 = (bp1, bp2)
else:
seq = mybasic.rc(r.seq(),'DNA')
offset = len(seq)-int(match.segL[0][1].split('..')[1])
bp12 = (bp2, bp1)
mybasic.addHash(seqH,bp12,(offset,seq))
seqL = seqH.items()
seqL.sort(lambda x,y: cmp(len(y[1]),len(x[1])))
for ((bp1,bp2), vL) in seqL:
vL.sort(lambda x,y: cmp(y[0],x[0]))
maxOffset = vL[0][0]
print '\n',bp1,bp2,len(vL),'\n'
for (offset,seq) in vL:
print '%s%s %s' % (' ' * (maxOffset-offset),seq[:offset],seq[offset:])
def loadRefFlatByChr(
refFlatFileName='/data1/Sequence/ucsc_hg19/annot/refFlat_splice_EGFR.txt'
):
h = {}
for line in open(refFlatFileName):
r = mygenome.processRefFlatLine(line)
mybasic.addHash(h, r['chrom'], r)
return h
def process_bp(inGsnapFileName,outBpFileName):
result = mygsnap.gsnapFile(inGsnapFileName,False)
outBpFile = open(outBpFileName, 'w')
seqH = {}
for r in result:
match = r.matchL()[0]
if not '(transloc)' in r.pairRel:
raise Exception
if len(match.segL) != 2:
raise Exception
s1 = match.segL[0][2]
s2 = match.segL[1][2]
if s1[0] != s2[0]:
raise Exception
strand = s1[0]
s1T = re.match('[+-]([^:]+):[0-9]+..([0-9]+)',s1).groups()
s2T = re.match('[+-]([^:]+):([0-9]+)..[0-9]+',s2).groups()
if strand == '+':
seq = r.seq()
offset = int(match.segL[0][1].split('..')[1])
junction = (s1T, s2T)
else:
seq = mybasic.rc(r.seq(),'DNA')
offset = len(seq)-int(match.segL[0][1].split('..')[1])
junction = (s2T, s1T)
mybasic.addHash(seqH,junction,(offset,seq))
for ((j1,j2), vL) in seqH.items():
vL.sort(lambda x,y: cmp(x[0],y[0]))
vL_mod = []
for (offset,seq) in vL:
offset = blockSize-offset+1
vL_mod.append('%s:%s' % (offset,seq))
outBpFile.write('%s:%s-%s,%s:%s-%s,%s\n' % (j1[0].split('_')[0],int(j1[1])-blockSize,j1[1], j1[0].split('_')[0],j1[1],int(j1[1])+blockSize, '|'.join(vL_mod)))
def loadRefFlatByChr(refFlatFileName='/Z/Sequence/ucsc_hg19/annot/refFlat.txt'):
h = {}
for line in open(refFlatFileName):
r = processRefFlatLine(line)
mybasic.addHash(h, r['chrom'], r)
if 'chrM' not in h:
h['chrM'] = []
return h
def loadAnnot(geneL=[]):
refFlatH = mygenome.loadRefFlatByChr()
eiH = {}
ei_keyH = {}
juncInfoH = {}
for chrom in refFlatH.keys():
eiH[chrom] = {}
juncInfoH[chrom] = {}
refFlatL = refFlatH[chrom]
for tH in refFlatL:
if geneL!=[] and tH['geneName'] not in geneL:
continue
for i in range(len(tH['exnList'])):
if tH['strand'] == '+':
pos = tH['exnList'][i][1]
e_num = i+1
else:
pos = tH['exnList'][i][0]
e_num = len(tH['exnList'])-i
mybasic.addHash(juncInfoH[chrom], pos, '%s%s:%s:%s/%s' % (tH['strand'], tH['geneName'], tH['refSeqId'], e_num, len(tH['exnList'])))
eiH[chrom][pos] = 0
ei_keyH[chrom] = eiH[chrom].keys()
ei_keyH[chrom].sort()
ei_cntH = {}
for chrom in juncInfoH.keys():
ei_cntH[chrom] = {}
i = 0
for pos in sorted(juncInfoH[chrom].keys()):
i += 1
ei_cntH[chrom][pos] = i
return eiH,ei_keyH,juncInfoH,ei_cntH
def parse(loc, juncInfo):
rm = re.match('([^:]+):([^:]+)', loc)
chrom, pos = rm.groups()
h = {}
for junc in juncInfo.split(','):
rm = re.match('([+-])([^:]+):[^:]+:(.*)\/(.*)', junc)
strand, geneN, exonIdx, exonTot = rm.groups()
if strand == '+':
locParsed = '%s%s:%s' % (strand, chrom, pos)
else:
locParsed = '%s%s:%s' % (strand, chrom, int(pos) + 1)
mybasic.addHash(h, (locParsed, geneN), junc)
parseL = []
for ((locParsed, geneN), juncL) in h.iteritems():
maxTrans = 0
isLastExon = True
for junc in juncL:
rm = re.match('([+-])([^:]+):[^:]+:(.*)\/(.*)', junc)
strand, geneN, exonIdx, exonTot = rm.groups()
if exonIdx != exonTot:
isLastExon = False
if int(exonTot) > maxTrans:
alias = '%s/%s' % (exonIdx, exonTot)
maxTrans = int(exonTot)
parseL.append((locParsed, geneN, alias, isLastExon, ','.join(juncL)))
return parseL
def parse(loc,juncInfo):
rm = re.match('([^:]+):([^:]+)',loc)
chrom, pos = rm.groups()
h = {}
for junc in juncInfo.split(','):
rm = re.match('([+-])([^:]+):[^:]+:(.*)\/(.*)',junc)
strand,geneN,exonIdx,exonTot = rm.groups()
if strand == '+':
locParsed = '%s%s:%s' % (strand,chrom,pos)
else:
locParsed = '%s%s:%s' % (strand,chrom,int(pos)+1)
mybasic.addHash(h,(locParsed,geneN),junc)
parseL = []
for ((locParsed,geneN),juncL) in h.iteritems():
maxTrans = 0
isLastExon = True
for junc in juncL:
rm = re.match('([+-])([^:]+):[^:]+:(.*)\/(.*)',junc)
strand,geneN,exonIdx,exonTot = rm.groups()
if exonIdx!=exonTot:
isLastExon = False
if int(exonTot) > maxTrans:
alias = '%s/%s' % (exonIdx,exonTot)
maxTrans = int(exonTot)
parseL.append((locParsed,geneN,alias,isLastExon,','.join(juncL)))
return parseL
def loadAnnot(geneL=[]):
refFlatH = mygenome.loadRefFlatByChr()
eiH = {}
ei_keyH = {}
juncInfoH = {}
for chrom in refFlatH.keys():
eiH[chrom] = {}
juncInfoH[chrom] = {}
refFlatL = refFlatH[chrom]
for tH in refFlatL:
if geneL!=[] and tH['geneName'] not in geneL:
continue
for i in range(len(tH['exnList'])):
if tH['strand'] == '+':
pos = tH['exnList'][i][1]
e_num = i+1
else:
pos = tH['exnList'][i][0]
e_num = len(tH['exnList'])-i
mybasic.addHash(juncInfoH[chrom], pos, '%s%s:%s:%s/%s' % (tH['strand'], tH['geneName'], tH['refSeqId'], e_num, len(tH['exnList'])))
eiH[chrom][pos] = 0
cursor.execute('replace into temp_table (chrom,pos) values ("%s",%s)' % (chrom,pos))
ei_keyH[chrom] = eiH[chrom].keys()
ei_keyH[chrom].sort()
return eiH,ei_keyH,juncInfoH
def main(dirPath):
fileNameL = filter(lambda x: re.match('.*TCGA-..-....-0..*\.bam',x), os.listdir(dirPath)) # normal sample, bam
fileNameTokL = map(lambda x: re.match('.*(TCGA-..-....)-...-..([DW]).*\.bam',x), fileNameL)
h = {}
for rm in fileNameTokL:
sN = rm.group(1)
type = rm.group(2)
if 'SOLiD' in rm.group(0):
type += '-SD'
elif 'IlluminaGA' in rm.group(0):
type += '-GA'
mybasic.addHash(h,sN,type)
for (sN,typeL) in h.iteritems():
typeL = list(set(typeL))
typeL.sort()
sys.stdout.write('%s\tXSeq_%s\n' % (sN,','.join(typeL)))
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 main(inDrugFileName,outDirName,outFileName,geneL='wg',cutoff=0.05, plottype='AUC', plot='FALSE', outPlotDirName='/home/heejin/DrugScreening/figure',seqType='WTS'):
if seqType == 'WES':
idH = WESidH
else:
idH = WTSidH
inFile = open(inDrugFileName)
drugH = {}
drugL = inFile.readline()[:-2].split(',')[1:]
for drug in drugL:
drugH[drug] = {}
for line in inFile:
dataH = {}
dataL = line[:-2].split(',')
sId = dataL[0]
for i in range(len(drugL)):
dataH[sId] = dataL[i+1]
drugH[drugL[i]].update(dataH)
con,cursor = mymysql.connectDB(db='common')
if geneL == 'wg':
cursor.execute('SELECT distinct geneName FROM refFlat_hg19')
geneL = [x for (x,) in cursor.fetchall()]
elif geneL == 'cs':
cursor.execute('SELECT distinct gene_sym FROM cs_gene')
geneL = [x for (x,) in cursor.fetchall()]
else:
geneL = geneL
# fusion
outFile = open(outFileName, 'w')
outFile.write('Drug\tGene\tp_twosided\tp_greater\tp_less\tD\tp_twosided2\tD2\twtN\tmutN\twt_sampN\tmut_sampN\twilcox_p\tttest_p\tmed_z.score\tmean_z.score\tAltInfo\n')
outFile.close()
con,cursor = mymysql.connectDB(db='ircr1')
dbIdL = idH.values()
cursor.execute('select distinct samp_id from rpkm_gene_expr')
procSampL = [x for (x,) in cursor.fetchall()]
for gN in geneL:
# if gN != 'MET':
# continue
tempFileName = '%s/temp4test.txt' % outDirName
tempFile = open(tempFileName, 'w')
tempFile.write('Drug\tGene\tds_id\tdb_id\tAUC\tAlt\n')
cursor.execute('SELECT samp_id,gene_sym1,gene_sym2,nReads/(nReads+nReads_w1) as maf FROM splice_fusion_AF \
where (gene_sym1 ="%s" or gene_sym2="%s") and nPos>2 and frame like "%s:Y%s" ' % (gN,gN,'%','%'))
result = cursor.fetchall()
mutH = {}
if len(result) == 0:
continue
for (dbId, gs, gs2, maf) in result:
try:
if float(maf) < cutoff:
continue
except:
continue
type = '%s_%s' % (gs,gs2)
#mutH[dbId] = (type,maf)
mybasic.addHash(mutH,dbId,(type,maf))
scr_idL = drugH[drugH.keys()[0]].keys()
for drug in drugH.keys():
for id in idH.keys():
if id not in scr_idL:
continue
if idH[id] not in procSampL:
continue
try:
Alt = mutH[idH[id]]
Alt = '/'.join(map(str,Alt))
except:
Alt = 'NA'
tempFile.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (drug, gN, id, idH[id], drugH[drug][id], Alt))
tempFile.close()
os.system('Rscript ~/JK1/NSL/HTS/drugRespByFus.R %s %s %s %s %s' % (tempFileName, outFileName,plot,outPlotDirName,plottype))
def main(inFileDir,outFileName):
outFile = open(outFileName,'w')
registry = []
inFileNameL = glob.glob('%s/*HumanMethylation*' % (inFileDir,))
inFileNameL.sort(lambda x,y: cmp(y,x))
for inFileName in inFileNameL:
sId = inFileName[inFileName.index('TCGA-'):inFileName.index('TCGA-')+28]
if sId in registry:
continue
registry.append(sId)
pId = sId[:12]
if int(sId[13:15])<10:
TN = 'T'
else:
TN = 'N'
if 'HumanMethylation450' in inFileName:
platform = 'Infinium450k'
else:
platform = 'Infinium27k'
print sId, platform
inFile = open(inFileName)
line = inFile.readline()
inFile.readline()
geneH = {}
for line in inFile:
tokL = line.rstrip().split('\t')
geneN = tokL[3]
value = tokL[2]
if not geneN or value=='NA':
continue
mybasic.addHash(geneH,geneN,float(value))
for geneN,valueL in geneH.iteritems():
v = numpy.mean(valueL)
for g in geneN.split(';'):
outFile.write('%s\t%s\t%s\t%s\t%s\t%.2f\n' % (platform,sId,pId,TN,g,v))
inFileNameL = glob.glob('%s/*OMA002*' % (inFileDir,))
platform = 'GoldenGate3k'
for inFileName in inFileNameL:
inFile = open(inFileName)
line = inFile.readline()
sId = line.rstrip().split('\t')[1]
if sId in registry:
continue
registry.append(sId)
pId = sId[:12]
if int(sId[13:15])<10:
TN = 'T'
else:
TN = 'N'
inFile.readline()
print sId, platform
geneH = {}
for line in inFile:
name,value = line.rstrip().split('\t')
geneN = name[:name.find('_')]
loc = name[name.find('_')+1:]
if not geneN or value=='N/A':
continue
mybasic.addHash(geneH,geneN,float(value))
for geneN,valueL in geneH.iteritems():
for g in geneN.split(';'):
outFile.write('%s\t%s\t%s\t%s\t%s\t%.2f\n' % (platform,sId,pId,TN,g,v))
def exonSkip_filter(inFileName, outFileName):
'''
filters-in exon-skipping candidates in splice-mapped gsnap
'''
result = mygsnap.gsnapFile(inFileName, False)
if outFileName[-3:] == '.gz':
outFile = gzip.open(outFileName, 'wb')
else:
outFile = open(outFileName, 'w')
count_all = 0
count_include = 0
for r in result:
if r.nLoci != 1:
continue
match = r.matchL()[0]
if len(match.segL) != 2:
continue
segObjL = match.getSegInfo()
jncH = {}
skip = False
for segObj in segObjL:
if segObj.span - segObj.numMatch > 2 or segObj.percMatch < 90 or segObj.span < 5:
skip = True
break
if segObj.label == '':
break
for b in segObj.label.split('|'):
rm2 = re.match('(.*)\.exon([0-9]+)\/[0-9]+', b)
transId = rm2.group(1)
exonNum = int(rm2.group(2))
mybasic.addHash(jncH, transId, exonNum)
if skip:
continue
jncL = jncH.items()
if len(jncL) > 0 and max([len(j[1]) for j in jncL]) > 1:
minDist = 100
for i in range(len(jncL)):
if len(jncL[i][1]) == 2 and abs(jncL[i][1][0] -
jncL[i][1][1]) < minDist:
minDist = abs(jncL[i][1][0] - jncL[i][1][1])
if minDist == 1: # only difference
outFile.write(r.rawText() + '\n')
count_include += 1
count_all += 1
print 'Results:', count_include, count_all
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 exonSkip_filter(inFileName,outFileName):
'''
filters-in exon-skipping candidates in splice-mapped gsnap
'''
result = mygsnap.gsnapFile(inFileName, False)
outFile = open(outFileName, 'w')
count_all = 0
count_include = 0
for r in result:
if r.nLoci != 1:
continue
match = r.matchL()[0]
if len(match.segL) != 2:
continue
segObjL = match.getSegInfo()
jncH = {}
skip = False
for segObj in segObjL:
if segObj.span - segObj.numMatch > 2 or segObj.percMatch < 90 or segObj.span < 5:
skip = True
break
if segObj.label == '':
break
for b in segObj.label.split('|'):
rm2 = re.match('(.*)\.exon([0-9]+)\/[0-9]+',b)
transId = rm2.group(1)
exonNum = int(rm2.group(2))
mybasic.addHash(jncH,transId,exonNum)
if skip:
continue
jncL = jncH.items()
if len(jncL)>0 and max([len(j[1]) for j in jncL])>1:
minDist = 100
for i in range(len(jncL)):
if len(jncL[i][1]) == 2 and abs(jncL[i][1][0]-jncL[i][1][1]) < minDist:
minDist = abs(jncL[i][1][0]-jncL[i][1][1])
if minDist > 1:
outFile.write(r.rawText()+'\n')
count_include += 1
count_all += 1
print 'Results:',count_include, count_all
def main(inFileDir, outFileName):
outFile = open(outFileName, 'w')
registry = []
inFileNameL = glob.glob('%s/*HumanMethylation*' % (inFileDir, ))
inFileNameL.sort(lambda x, y: cmp(y, x))
for inFileName in inFileNameL:
sId = inFileName[inFileName.index('TCGA-'):inFileName.index('TCGA-') +
28]
if sId in registry:
continue
registry.append(sId)
pId = sId[:12]
if int(sId[13:15]) < 10:
TN = 'T'
else:
TN = 'N'
if 'HumanMethylation450' in inFileName:
platform = 'Infinium450k'
else:
platform = 'Infinium27k'
print sId, platform
inFile = open(inFileName)
line = inFile.readline()
inFile.readline()
geneH = {}
for line in inFile:
tokL = line.rstrip().split('\t')
geneN = tokL[3]
value = tokL[2]
if not geneN or value == 'NA':
continue
mybasic.addHash(geneH, geneN, float(value))
for geneN, valueL in geneH.iteritems():
v = numpy.mean(valueL)
for g in geneN.split(';'):
outFile.write('%s\t%s\t%s\t%s\t%s\t%.2f\n' %
(platform, sId, pId, TN, g, v))
inFileNameL = glob.glob('%s/*OMA002*' % (inFileDir, ))
platform = 'GoldenGate3k'
for inFileName in inFileNameL:
inFile = open(inFileName)
line = inFile.readline()
sId = line.rstrip().split('\t')[1]
if sId in registry:
continue
registry.append(sId)
pId = sId[:12]
if int(sId[13:15]) < 10:
TN = 'T'
else:
TN = 'N'
inFile.readline()
print sId, platform
geneH = {}
for line in inFile:
name, value = line.rstrip().split('\t')
geneN = name[:name.find('_')]
loc = name[name.find('_') + 1:]
if not geneN or value == 'N/A':
continue
mybasic.addHash(geneH, geneN, float(value))
for geneN, valueL in geneH.iteritems():
for g in geneN.split(';'):
outFile.write('%s\t%s\t%s\t%s\t%s\t%.2f\n' %
(platform, sId, pId, TN, g, v))
