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first working DMS class

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Eric Coissac
2016-12-27 06:17:45 +01:00
parent 62caf1346e
commit 0526386337
14 changed files with 371 additions and 259 deletions
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62
python/obitools3/parsers/fasta.pyx
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@ -6,8 +6,12 @@ Created on 30 mars 2016
@author: coissac
'''
#from obitools3.dms._obiseq cimport OBI_Seq
def fastaIterator(lineiterator, int buffersize=100000000):
def fastaIterator(lineiterator,
int buffersize=100000000
):
cdef LineBuffer lb
cdef str ident
cdef str definition
@ -15,6 +19,7 @@ def fastaIterator(lineiterator, int buffersize=100000000):
cdef list s
cdef bytes sequence
cdef bytes quality
# cdef OBI_Seq seq
if isinstance(lineiterator,(str,bytes)):
lineiterator=uopen(lineiterator)
@ -41,7 +46,60 @@ def fastaIterator(lineiterator, int buffersize=100000000):
sequence = b"".join(s)
quality = None
# seq = OBI_Seq(id,
# sequence,
# definition,
# tags=tags,
# )
yield { "id" : ident,
"definition" : definition,
"sequence" : sequence,
"quality" : quality,
"tags" : tags,
"annotation" : {}
}
def fastaNucIterator(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
# cdef OBI_Seq seq
if isinstance(lineiterator,(str,bytes)):
lineiterator=uopen(lineiterator)
if isinstance(lineiterator, LineBuffer):
lb=lineiterator
else:
lb=LineBuffer(lineiterator,buffersize)
i = iter(lb)
line = next(i)
while True:
ident,tags,definition = parseHeader(line)
s = []
line = next(i)
try:
while line[0]!='>':
s.append(str2bytes(line)[0:-1])
line = next(i)
except StopIteration:
pass
sequence = b"".join(s)
quality = None
# seq =
yield { "id" : ident,
"definition" : definition,
"sequence" : sequence,