def updateSequence(oFN, oFF, extend, assembly): NX = Nexus(oFN, oFF) NX.load(['sequence', 'tcc']) gf = GenomeFetch.GenomeFetch(assembly) while NX.nextID(): chrom, strand, start, end = bioLibCG.tccSplit(NX.tcc) start, end = start - extend, end + extend newTcc = bioLibCG.makeTcc(chrom, strand, start, end) NX.sequence = gf.getSequence(newTcc) NX.save()
def updateSequence(oFN, oFF, extend, assembly): NX = Nexus(oFN, oFF) NX.load(['sequence', 'tcc']) gf = GenomeFetch.GenomeFetch(assembly) while NX.nextID(): chrom, strand, start, end = bioLibCG.tccSplit(NX.tcc) start, end = start - extend, end + extend newTcc = bioLibCG.makeTcc(chrom, strand, start, end) NX.sequence = gf.getSequence(newTcc) NX.save()
def updateSimSeqsForUnique(oFN, oFF, seqFN): NX = Nexus(oFN, oFF) NX.load(['sequence']) id_seq = {} f = open(seqFN, 'r') for line in f: ls = line.strip().split('\t') id_seq[int(ls[0])] = ls[1] f.close() while NX.nextID(): NX.sequence = id_seq.get(NX.id, '.') NX.save()
def updateSimSeqsForUnique(oFN, oFF, seqFN): NX = Nexus(oFN, oFF) NX.load(['sequence']) id_seq = {} f = open(seqFN, 'r') for line in f: ls = line.strip().split('\t') id_seq[int(ls[0])] = ls[1] f.close() while NX.nextID(): NX.sequence = id_seq.get(NX.id, '.') NX.save()