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()