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Cython: fasta writer

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This commit is contained in:
Celine Mercier
2018-10-09 16:40:30 +02:00
parent e31c8ea57a
commit aa5ee53478
2 changed files with 13 additions and 15 deletions
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2
python/obitools3/format/fasta.pxd
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@ -4,7 +4,7 @@ from cython.view cimport array as cvarray
cdef class FastaFormat: cdef class FastaFormat:
cdef HeaderFormat headerFormater cdef HeaderFormat headerFormatter
cdef size_t sequenceBufferLength cdef size_t sequenceBufferLength
cdef char* sequenceBuffer cdef char* sequenceBuffer

22
python/obitools3/format/fasta.pyx
View File

@ -1,17 +1,22 @@
#cython: language_level=3
cimport cython cimport cython
from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN
from obitools3.utils cimport bytes2str
cdef class FastaFormat: cdef class FastaFormat:
def __init__(self, list tags=[], bint printNAKeys=False): def __init__(self, list tags=[], bint printNAKeys=False):
self.headerFormater = HeaderFormat(True, self.headerFormatter = HeaderFormat("fasta",
tags, tags,
printNAKeys) printNAKeys)
@cython.boundscheck(False) @cython.boundscheck(False)
def __call__(self, dict data): def __call__(self, object data):
cdef bytes brawseq = data['sequence'] cdef bytes brawseq = data[NUC_SEQUENCE_COLUMN]
cdef size_t lseq = len(brawseq) cdef size_t lseq = len(brawseq)
cdef size_t k=0 cdef size_t k = 0
cdef list lines = [] cdef list lines = []
for k in range(0,lseq,60): for k in range(0,lseq,60):
@ -19,12 +24,5 @@ cdef class FastaFormat:
brawseq = b'\n'.join(lines) brawseq = b'\n'.join(lines)
return "%s\n%s" % (self.headerFormater(data),bytes2str(brawseq)) return bytes2str(self.headerFormatter(data) + b"\n" + brawseq)