def extractBaitSeq(baitSeq, baitRev, genome, coord):
fs = open(baitSeq, "w")
fr = open(baitRev, "w")
for name, seq in readFasta(genome):
c = editBaitCoord(coord.get(name, []), 200)
if not c:
continue
for n, s in extractSeq(name, c, seq, True):
beg, end = n.split(":")[1:]
n = ">" + name + ":" + ",".join(beg.split(",")[1:-1]) + ":" + ",".join(end.split(",")[1:-1])
writeFasta(n, s, fs)
writeFasta(n, s[::-1], fr)
fs.close()
fr.close()
def extractBaitSeq(baitSeq, baitRev, genome, coord):
fs = open(baitSeq, "w")
fr = open(baitRev, "w")
for name, seq in readFasta(genome):
c = editBaitCoord(coord.get(name, []), 200)
if not c: continue
for n, s in extractSeq(name, c, seq, True):
beg, end = n.split(":")[1:]
n = ">" + name + ":" + \
",".join(beg.split(",")[1:-1]) + ":" + \
",".join(end.split(",")[1:-1])
writeFasta(n, s, fs)
writeFasta(n, s[::-1], fr)
fs.close()
fr.close()
def extractFlankSeq(flankSeq, flankRev, flanklen, hitDict, nucleus):
fs = open(flankSeq, "w")
fr = open(flankRev, "w")
wrote = 0
mark = string.maketrans(":", "^")
for name, seq in readFasta(nucleus):
coord = makeFlankCoord(hitDict.get(name, []), flanklen)
if not coord: continue
for n, s in extractSeq(name, coord, seq, True):
beg, end = n.split(":")[1:]
n = ">" + name.translate(mark) + ":" + \
beg.split(",")[-1] + ":" + end.split(",")[0]
if len(s):
writeFasta(n, s, fs)
writeFasta(n, s[::-1], fr)
wrote += 1
fs.close()
fr.close()
return wrote
def extractFlankSeq(flankSeq, flankRev, flanklen, hitDict, nucleus):
fs = open(flankSeq, "w")
fr = open(flankRev, "w")
wrote = 0
mark = string.maketrans(":", "^")
for name, seq in readFasta(nucleus):
coord = makeFlankCoord(hitDict.get(name, []), flanklen)
if not coord: continue
for n, s in extractSeq(name, coord, seq, True):
beg, end = n.split(":")[1:]
n = ">" + name.translate(mark) + ":" + \
beg.split(",")[-1] + ":" + end.split(",")[0]
if len(s):
writeFasta(n, s, fs)
writeFasta(n, s[::-1], fr)
wrote += 1
fs.close()
fr.close()
return wrote
