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Cython API: Various fixes in input handlers (parsers, openers etc).

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Mostly working but not bug-free
This commit is contained in:
Celine Mercier
2017-08-20 17:37:51 +02:00
parent c559ddf487
commit 74f15d1a23
4 changed files with 75 additions and 67 deletions
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28
python/obitools3/uri/decode.pyx
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@ -364,19 +364,22 @@ def open_uri(uri,
if qualifiers[b"seqtype"]==b"nuc":
objclass = Nuc_Seq
if format==b"fasta":
iseq = fastaNucIterator(file,skip,only)
iseq = fastaNucIterator(file,
skip=skip,
only=only)
elif format==b"fastq":
iseq = fastqIterator(file,
skip,only,
offset,
noquality)
skip=skip,
only=only,
offset=offset,
noquality=noquality)
else:
raise NotImplementedError('Sequence file format not implemented')
elif qualifiers[b"seqtype"]==b"prot":
raise NotImplementedError()
else:
iseq,objclass = entryIteratorFactory(file,
skip,only,
skip, only,
seqtype,
offset,
noquality,
@ -388,13 +391,12 @@ def open_uri(uri,
stripwhite,
blanklineskip,
commentchar)
tmpdms = get_temp_dms()
return (file,iseq,objclass,urib)
#tmpdms = get_temp_dms()
return (file, iseq, objclass, urib)