def gnuc_roll_left_del(chrm, beg, end):
""" beg and end are 1st and last base in the deleted sequence """
sb = faidx.SeqBuf(chrm, beg)
while True:
if beg <= 1:
break
left_base = sb.get_base(chrm, beg - 1)
rightmost = sb.get_base(chrm, end)
if left_base == 'N' or rightmost == 'N':
break
if left_base != rightmost:
break
beg -= 1
end -= 1
return beg, end
def gnuc_roll_left_ins(chrm, pos, gnuc_insseq):
""" pos is where insertion occur after """
sb = faidx.SeqBuf(chrm, pos)
_gnuc_insseq_ = deque(gnuc_insseq)
while True:
if pos <= 1:
break
left_base = sb.get_base(chrm, pos)
rightmost = _gnuc_insseq_[-1]
if left_base == 'N' or rightmost == 'N':
break
if left_base != rightmost:
break
_gnuc_insseq_.pop()
_gnuc_insseq_.appendleft(left_base)
pos -= 1
return pos, ''.join(_gnuc_insseq_)
def gnuc_roll_right_ins(chrm, pos, gnuc_insseq):
""" pos is where insertion occur after """
sb = faidx.SeqBuf(chrm, pos)
chrmlen = faidx.refgenome.chrm2len(chrm)
_gnuc_insseq_ = deque(gnuc_insseq)
while True:
if pos + 1 >= chrmlen:
break
right_base = sb.get_base(chrm, pos + 1)
leftmost = _gnuc_insseq_[0]
if right_base == 'N' or leftmost == 'N':
break
if right_base != leftmost:
break
_gnuc_insseq_.popleft()
_gnuc_insseq_.append(right_base)
pos += 1
return pos, ''.join(_gnuc_insseq_)
def gnuc_roll_right_del(chrm, beg, end):
""" beg and end are 1st and last base in the deleted sequence """
sb = faidx.SeqBuf(chrm, end)
chrmlen = faidx.refgenome.chrm2len(chrm)
while True:
# check end of chromosome
if end + 1 >= chrmlen:
break
right_base = sb.get_base(chrm, end + 1)
leftmost = sb.get_base(chrm, beg)
if right_base == 'N' or leftmost == 'N':
break
if right_base != leftmost:
break
beg += 1
end += 1
return beg, end