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Merge branch 'master' into Eric_version_for_sequence

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Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx
This commit is contained in:
Eric Coissac
2016-08-03 10:09:20 +02:00
parent 448fa8d325 000b9999ad
commit 8f0462c407
31 changed files with 1142 additions and 953 deletions
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1
python/obitools3/parsers/fasta.pxd
View File

@ -1,5 +1,6 @@
#cython: language_level=3
from ..utils cimport str2bytes
from .header cimport parseHeader
from ..files.universalopener cimport uopen
from ..files.linebuffer cimport LineBuffer

7
python/obitools3/parsers/fasta.pyx
View File

@ -6,12 +6,15 @@ Created on 30 mars 2016
@author: coissac
'''
def fastaIterator(lineiterator, int buffersize=100000000):
cdef LineBuffer lb
cdef str ident
cdef str definition
cdef dict tags
cdef list s
cdef bytes sequence
cdef bytes quality
if isinstance(lineiterator,(str,bytes)):
lineiterator=uopen(lineiterator)
@ -31,12 +34,12 @@ def fastaIterator(lineiterator, int buffersize=100000000):
try:
while line[0]!='>':
s.append(line[0:-1])
s.append(str2bytes(line)[0:-1])
line = next(i)
except StopIteration:
pass
sequence = "".join(s)
sequence = b"".join(s)
quality = None
yield { "id" : ident,

2
python/obitools3/parsers/fastq.pxd
View File

@ -1,5 +1,7 @@
#cython: language_level=3
from ..utils cimport str2bytes
from .header cimport parseHeader
from ..files.universalopener cimport uopen
from ..files.linebuffer cimport LineBuffer

10
python/obitools3/parsers/fastq.pyx
View File

@ -6,15 +6,13 @@ Created on 30 mars 2016
@author: coissac
'''
def fastqIterator(lineiterator, int buffersize=100000000):
cdef LineBuffer lb
cdef str ident
cdef str definition
cdef dict tags
cdef bytes sequence
cdef bytes quality
if isinstance(lineiterator,(str,bytes)):
lineiterator=uopen(lineiterator)
@ -27,9 +25,9 @@ def fastqIterator(lineiterator, int buffersize=100000000):
i = iter(lb)
for line in i:
ident,tags,definition = parseHeader(line)
sequence = next(i)[0:-1]
sequence = str2bytes(next(i)[0:-1])
next(i)
quality = next(i)[0:-1]
quality = str2bytes(next(i)[0:-1])
yield { "id" : ident,
"definition" : definition,