Added genbank parser

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

View File

@ -6,6 +6,7 @@ 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)
@ -135,6 +136,15 @@ def entryIteratorFactory(lineiterator,
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')