def updateGeneName(dFN,
fFN,
wigDir,
chrom,
strand,
prefix,
switchStrand=False):
NX = Nexus(dFN, fFN)
NX.load(['geneNames', 'tcc'])
if switchStrand:
strand = -strand
strand = str(strand)
coord_gName = cgWig.loadSingleWigTranscript(wigDir, chrom, strand, prefix)
while NX.nextID():
chrom, strand, start, end = bioLibCG.tccSplit(NX.tcc)
overlappingGenes = coord_gName.get(start, ".")
if overlappingGenes == "NONE":
NX.geneNames = []
else:
NX.geneNames = overlappingGenes.split(',')
NX.save()
def updateTranscriptOverlap(oFN, wigDir, chrom, strand, rn = None, tn = None):
oNX = cgNexusFlat.Nexus(oFN, cgDegPeak.Peak)
oNX.load(['tOverlap', 'tcc'], [rn, tn])
#load the AS wig file for this degradome strand
if strand == '1':
strand = '-1'
else:
strand = '1'
coord_transcripts = cgWig.loadSingleWigTranscript(wigDir, chrom, strand, 'transcript')
for oID in oNX.tOverlap:
tChrom, tStrand, start, end = bioLibCG.tccSplit(oNX.tcc[oID])
if tStrand == '1':
tStrand = '-1'
else:
tStrand = '1'
if tChrom != chrom or tStrand != strand: continue
oNX.tOverlap[oID] = False
for i in xrange(start, end + 1):
if i in coord_transcripts:
oNX.tOverlap[oID] = True
break
oNX.save()
def updateTranscriptOverlap(oFN, wigDir, chrom, strand, rn=None, tn=None):
oNX = cgNexusFlat.Nexus(oFN, cgDegPeak.Peak)
oNX.load(['tOverlap', 'tcc'], [rn, tn])
#load the AS wig file for this degradome strand
if strand == '1':
strand = '-1'
else:
strand = '1'
coord_transcripts = cgWig.loadSingleWigTranscript(wigDir, chrom, strand,
'transcript')
for oID in oNX.tOverlap:
tChrom, tStrand, start, end = bioLibCG.tccSplit(oNX.tcc[oID])
if tStrand == '1':
tStrand = '-1'
else:
tStrand = '1'
if tChrom != chrom or tStrand != strand: continue
oNX.tOverlap[oID] = False
for i in xrange(start, end + 1):
if i in coord_transcripts:
oNX.tOverlap[oID] = True
break
oNX.save()
def updateGeneName(dFN, fFN, wigDir, chrom, strand, prefix, switchStrand = False):
NX = Nexus(dFN, fFN)
NX.load(['geneNames', 'tcc'])
if switchStrand:
strand = -strand
strand = str(strand)
coord_gName = cgWig.loadSingleWigTranscript(wigDir, chrom, strand, prefix)
while NX.nextID():
chrom, strand, start, end = bioLibCG.tccSplit(NX.tcc)
overlappingGenes = coord_gName.get(start, ".")
if overlappingGenes == "NONE":
NX.geneNames = []
else:
NX.geneNames = overlappingGenes.split(',')
NX.save()