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()
