1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
|
#cython: language_level=3
cimport cython
from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN
from obitools3.utils cimport bytes2str
cdef class FastaFormat:
def __init__(self, list tags=[], bint printNAKeys=False, bytes NAString=b"NA", bint NAIntTo0=False):
self.headerFormatter = HeaderFormat("fasta",
tags=tags,
printNAKeys=printNAKeys,
NAString=NAString,
NAIntTo0=NAIntTo0)
@cython.boundscheck(False)
def __call__(self, object data):
cdef bytes brawseq = data[NUC_SEQUENCE_COLUMN]
cdef size_t lseq = len(brawseq)
cdef size_t k = 0
cdef list lines = []
for k in range(0,lseq,60):
lines.append(brawseq[k:(k+60)])
brawseq = b'\n'.join(lines)
return self.headerFormatter(data) + b"\n" + brawseq
|
