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|
#cython: language_level=3
'''
Created on 30 mars 2016
@author: coissac
'''
from obitools3.dms.obiseq cimport Nuc_Seq
def fastqIterator(lineiterator,
int skip=0,
only=None,
int offset=-1,
bint noquality=False,
firstline=None,
int buffersize=100000000,
bytes nastring=b"NA"
):
if noquality:
return fastqWithoutQualityIterator(lineiterator,
skip,only,
firstline,
buffersize,
nastring)
else:
return fastqWithQualityIterator(lineiterator,
skip,only,
offset,
firstline,
buffersize,
nastring)
def fastqWithQualityIterator(lineiterator,
int skip=0,
only=None,
int offset=-1,
firstline=None,
int buffersize=100000000,
bytes nastring=b"NA"
):
cdef LineBuffer lb
cdef bytes ident
cdef bytes definition
cdef dict tags
cdef bytes sequence
cdef bytes quality
cdef int skipped, lines_to_skip, ionly, read, j
if only is None:
ionly=-1
else:
ionly=int(only)
if isinstance(lineiterator, (str, bytes)):
lineiterator=uopen(lineiterator)
if isinstance(lineiterator, LineBuffer):
iterator = iter(lineiterator)
else:
if hasattr(lineiterator, "readlines"):
iterator = iter(LineBuffer(lineiterator, buffersize))
elif hasattr(lineiterator, '__next__'):
iterator = lineiterator
else:
raise Exception("Invalid line iterator")
i = iterator
lines_to_skip = skip*4 - (firstline is not None)
for skipped in range(lines_to_skip):
next(i)
if skip > 0:
firstline=None
read=0
if firstline is None:
hline = next(i)
else:
hline = firstline
for line in i:
if ionly >= 0 and read >= ionly:
break
ident,tags,definition = parseHeader(hline, nastring=nastring)
sequence = line[0:-1]
next(i)
quality = next(i)[0:-1]
seq = Nuc_Seq(ident,
sequence,
definition=definition,
quality=quality,
offset=offset,
tags=tags)
yield seq
read+=1
try:
hline = next(i)
except StopIteration:
return
def fastqWithoutQualityIterator(lineiterator,
int skip=0,
only=None,
firstline=None,
int buffersize=100000000,
bytes nastring=b"NA"
):
cdef bytes ident
cdef bytes definition
cdef dict tags
cdef bytes sequence
cdef bytes quality
cdef int skipped, lines_to_skip, ionly, read
cdef int j
if only is None:
ionly=-1
else:
ionly=int(only)
if isinstance(lineiterator, (str, bytes)):
lineiterator=uopen(lineiterator)
if isinstance(lineiterator, LineBuffer):
iterator = iter(lineiterator)
else:
if hasattr(lineiterator, "readlines"):
iterator = iter(LineBuffer(lineiterator, buffersize))
elif hasattr(lineiterator, '__next__'):
iterator = lineiterator
else:
raise Exception("Invalid line iterator")
i = iterator
lines_to_skip = skip*4 - (firstline is not None)
for skipped in range(lines_to_skip):
next(i)
if skip > 0:
firstline=None
read=0
if firstline is None:
hline = next(i)
else:
hline = firstline
for line in i:
if ionly >= 0 and read >= ionly:
break
ident,tags,definition = parseHeader(hline, nastring=nastring)
sequence = line[0:-1]
next(i)
next(i)
seq = Nuc_Seq(ident,
sequence,
definition=definition,
quality=None,
offset=-1,
tags=tags)
yield seq
read+=1
try:
hline = next(i)
except StopIteration:
return
|
