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Bug fix with byte strings in Python3

This commit is contained in:
martinghunt 2017-11-09 13:57:15 +00:00
parent a7b38f6900
commit 29a26e3eea
1 changed files with 6 additions and 3 deletions
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9
python/mappy.pyx
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@ -13,7 +13,8 @@ cdef class Alignment:
cdef _ctg, _cigar # these are python objects cdef _ctg, _cigar # these are python objects
def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand): def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand):
self._ctg, self._ctg_len, self._r_st, self._r_en = str(ctg), cl, cs, ce self._ctg = ctg if isinstance(ctg, str) else ctg.decode()
self._ctg_len, self._r_st, self._r_en = cl, cs, ce
self._strand, self._q_st, self._q_en = strand, qs, qe self._strand, self._q_st, self._q_en = strand, qs, qe
self._NM, self._mlen, self._blen = NM, mlen, blen self._NM, self._mlen, self._blen = NM, mlen, blen
self._mapq = mapq self._mapq = mapq
@ -150,9 +151,11 @@ def fastx_read(fn):
ks = cmappy.mm_fastx_open(str.encode(fn)) ks = cmappy.mm_fastx_open(str.encode(fn))
if ks is NULL: return None if ks is NULL: return None
while cmappy.kseq_read(ks) >= 0: while cmappy.kseq_read(ks) >= 0:
if ks.qual.l > 0: qual = str(ks.qual.s) if ks.qual.l > 0: qual = ks.qual.s if isinstance(ks.qual.s, str) else ks.qual.s.decode()
else: qual = None else: qual = None
yield str(ks.name.s), str(ks.seq.s), qual name = ks.name.s if isinstance(ks.name.s, str) else ks.name.s.decode()
seq = ks.seq.s if isinstance(ks.seq.s, str) else ks.seq.s.decode()
yield name, seq, qual
cmappy.mm_fastx_close(ks) cmappy.mm_fastx_close(ks)
def verbose(v=None): def verbose(v=None):