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Bug fixes for input handlers, openers, parsers etc. Compiling but not

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tested
This commit is contained in:
Celine Mercier
2017-07-27 19:42:44 +02:00
parent b2fc1f4611
commit 7112f44fb7
4 changed files with 32 additions and 17 deletions
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5
python/obitools3/parsers/fastq.pyx
View File

@ -6,11 +6,14 @@ Created on 30 mars 2016
@author: coissac
'''
from obitools3.dms.obiseq import Nuc_Seq
def fastqIterator(lineiterator,
int skip=0,
only=None,
int qualityoffset=-1,
bool noquality=False,
bint noquality=False,
firstline=None,
int buffersize=100000000
):

7
python/obitools3/parsers/universal.pxd Normal file
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@ -0,0 +1,7 @@
#cython: language_level=3
from ..utils cimport str2bytes
from ..files.universalopener cimport uopen
from ..files.linebuffer cimport LineBuffer
from obitools3.dms.obiseq cimport Nuc_Seq

6
python/obitools3/uri/decode.pxd Normal file
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@ -0,0 +1,6 @@
#cython: language_level=3
from obitools3.dms.dms cimport DMS
from obitools3.dms.view.view cimport View
from obitools3.dms.column.column cimport Column
from obitools3.dms.taxo.taxo cimport Taxonomy

31
python/obitools3/uri/decode.pyx
View File

@ -1,12 +1,11 @@
from urllib.parse import urlparse, parse_qs, ParseResultBytes
#cython: language_level=3
from urllib.parse import urlparse, urlunparse, parse_qs, ParseResultBytes
from os.path import isdir, isfile, basename, join
from obitools3.utils import tobytes
from obitools3.dms.dms import DMS
from obitools3.dms.view.view import View
from obitools3.dms.column.column import Column
from obitools3.dms.taxo import Taxonomy
from obitools3.files.universalopener import uopen
from obitools3.parsers.fasta import fastaNucIterator
@ -15,7 +14,7 @@ from obitools3.parsers.universal import entryIteratorFactory
from obitools3.dms.obiseq import Nuc_Seq
cdef class MalformedURIException(RuntimeError):
class MalformedURIException(RuntimeError):
pass
cdef open_dms(bytes path,create=False):
@ -30,10 +29,10 @@ cdef open_dms(bytes path,create=False):
while(pos>0):
pos = path.find(b"/",pos)
if pos>0:
dirpath=path[0:pos]
dmspath=path[0:pos]
else:
dirpath=path
if not isdir(dirpath):
dmspath=path
if not isdir(dmspath):
dmsdirname=dmspath+b".obidms"
if isdir(dmsdirname):
dmsname=basename(dmspath)
@ -70,7 +69,7 @@ def open_dms_element(DMS dms, bytes path):
if len(path_parts) == 2:
taxon=taxo[int(path_parts[2])]
return (dms,taxon)
elif (len(path_parts) > 2:
elif len(path_parts) > 2:
raise MalformedURIException('Malformed Taxonomy URI')
return (dms,taxo)
@ -148,7 +147,7 @@ def open_uri(uri,input=True,config={}):
scheme=b'file'
dms = open_dms(urip.path)
if dms is None and default_dms is not None:
dms=(default_dms,urip.path))
dms=(default_dms,urip.path)
if dms is not None:
@ -198,7 +197,7 @@ def open_uri(uri,input=True,config={}):
seqtype=config["obi"]["seqtype"]
if b'skip' in qualifiers:
skip=int(qualifiers[b"skip"][0]
skip=int(qualifiers[b"skip"][0])
else:
skip=config["obi"]["skeep"]
if skip < 0:
@ -290,16 +289,16 @@ def open_uri(uri,input=True,config={}):
raise MalformedURIException('Malformed blanklineskip argument in URI')
if b"commentchar" in qualifiers:
nastring=qualifiers[b"commentchar"][0][0]
commentchar=qualifiers[b"commentchar"][0][0]
else:
nastring=config["obi"]["commentchar"]
commentchar=config["obi"]["commentchar"]
if format is not None:
if qualifiers[b"seqtype"]==b"nuc":
objclass = Nuc_Seq
if format="fasta":
if format==b"fasta":
iseq = fastaNucIterator(file,skip,only)
elif format="fastq":
elif format==b"fastq":
iseq = fastqIterator(file,
skip,only,
offset,
@ -309,7 +308,7 @@ def open_uri(uri,input=True,config={}):
elif qualifiers[b"seqtype"]==b"prot":
raise NotImplementedError()
else:
iseq,objclass = entryIterator(file,
iseq,objclass = entryIteratorFactory(file,
skip,only,
seqtype,
offset,