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#cython: language_level=3
import re
from obitools3.parsers.fasta import fastaNucIterator
from obitools3.parsers.fastq import fastqIterator
from obitools3.parsers.tab import tabIterator
from obitools3.parsers.ngsfilter import ngsfilterIterator
from obitools3.parsers.embl import emblIterator
from obitools3.parsers.genbank import genbankIterator
oligore = re.compile(b"^[ACGTRYSWKMBDHVN]+$",re.I)
tagre = re.compile(b"^([ACGTRYSWKMBDHVN]+|-)(:([ACGTRYSWKMBDHVN]+)|-)?$",re.I)
def is_ngsfilter_line(line): # TODO doesn't work?
try:
parts = line.split()
ok = tagre.match(parts[2])
ok&= oligore.match(parts[3])
ok&= oligore.match(parts[4])
ok&= parts[5]==b"F" | parts[5]==b"T"
return ok
except:
return False
def entryIteratorFactory(lineiterator,
int skip=0,
only=None,
bytes seqtype=b'nuc',
int offset=-1,
bint noquality=False,
bint skiperror=True,
bint header=False,
bytes sep=None,
bytes dec=b'.',
bytes nastring=b"NA",
bint stripwhite=True,
bint blanklineskip=True,
bytes commentchar=b"#",
int buffersize=100000000):
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
try:
first=next(i)
except StopIteration:
first=""
pass
format=b"tabular"
try:
if first[:1]==b">":
format=b"fasta"
if first[:1]==b"@":
format=b"fastq"
elif first[0:3]==b'ID ':
format=b"embl"
elif first[0:6]==b'LOCUS ':
format=b"genbank"
elif first[0:8]==b'#@ecopcr':
format=b"ecopcrfile"
elif is_ngsfilter_line(first):
format=b"ngsfilter"
except IndexError:
pass
# TODO Temporary fix
first=None
lineiterator.seek(0)
if format==b'fasta':
if seqtype == b'nuc':
return (fastaNucIterator(lineiterator,
skip=skip,only=only,
firstline=first,
buffersize=buffersize,
nastring=nastring),
Nuc_Seq,
format)
else:
raise NotImplementedError()
elif format==b'fastq':
return (fastqIterator(lineiterator,
skip=skip,only=only,
offset=offset,
noquality=noquality,
firstline=first,
buffersize=buffersize,
nastring=nastring),
Nuc_Seq,
format)
elif format==b'tabular':
return (tabIterator(lineiterator,
header = header,
sep = sep,
dec = dec,
stripwhite = stripwhite,
blanklineskip = blanklineskip,
commentchar = commentchar,
nastring=nastring,
skip = skip,
only = only,
firstline=first,
buffersize=buffersize),
dict,
format)
elif format==b'ngsfilter':
return (ngsfilterIterator(lineiterator,
sep = sep,
dec = dec,
stripwhite = stripwhite,
blanklineskip = blanklineskip,
commentchar = commentchar,
nastring=nastring,
skip = skip,
only = only,
firstline=first,
buffersize=buffersize),
dict,
format)
elif format==b'embl':
return (emblIterator(lineiterator,
skip=skip,
only=only,
firstline=first,
buffersize=buffersize),
Nuc_Seq,
format)
elif format==b'genbank':
return (genbankIterator(lineiterator,
skip=skip,
only=only,
firstline=first,
buffersize=buffersize),
Nuc_Seq,
format)
raise NotImplementedError('File format iterator not implemented yet')
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