obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Added genbank parser

Browse Source
This commit is contained in:
Celine Mercier
2019-03-15 16:06:27 +01:00
parent e8090a44c9
commit 7e20870719
2 changed files with 18 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
python/obitools3/parsers/universal.pyx
View File

@ -6,6 +6,7 @@ from obitools3.parsers.fastq import fastqIterator
from obitools3.parsers.tab import tabIterator from obitools3.parsers.tab import tabIterator
from obitools3.parsers.ngsfilter import ngsfilterIterator from obitools3.parsers.ngsfilter import ngsfilterIterator
from obitools3.parsers.embl import emblIterator from obitools3.parsers.embl import emblIterator
from obitools3.parsers.genbank import genbankIterator
oligore = re.compile(b"^[ACGTRYSWKMBDHVN]+$",re.I) oligore = re.compile(b"^[ACGTRYSWKMBDHVN]+$",re.I)
@ -135,6 +136,15 @@ def entryIteratorFactory(lineiterator,
buffersize=buffersize), buffersize=buffersize),
Nuc_Seq, Nuc_Seq,
format) 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') raise NotImplementedError('File format iterator not implemented yet')

8
python/obitools3/uri/decode.pyx
View File

@ -10,6 +10,7 @@ from obitools3.parsers.fastq import fastqIterator
from obitools3.parsers.tab import tabIterator from obitools3.parsers.tab import tabIterator
from obitools3.parsers.ngsfilter import ngsfilterIterator from obitools3.parsers.ngsfilter import ngsfilterIterator
from obitools3.parsers.embl import emblIterator from obitools3.parsers.embl import emblIterator
from obitools3.parsers.genbank import genbankIterator
from obitools3.parsers.universal import entryIteratorFactory from obitools3.parsers.universal import entryIteratorFactory
from obitools3.writers.fasta import FastaNucWriter from obitools3.writers.fasta import FastaNucWriter
@ -478,6 +479,13 @@ def open_uri(uri,
only=only) only=only)
else: else:
raise NotImplementedError('Output sequence file format not implemented') raise NotImplementedError('Output sequence file format not implemented')
elif format==b"genbank":
if input:
iseq = genbankIterator(file,
skip=skip,
only=only)
else:
raise NotImplementedError('Output sequence file format not implemented')
else: else:
raise NotImplementedError('Sequence file format not implemented') raise NotImplementedError('Sequence file format not implemented')
elif seqtype==b"prot": elif seqtype==b"prot":