diff --git a/python/obitools3/parsers/universal.pyx b/python/obitools3/parsers/universal.pyx index 4366e1d..4ef828f 100755 --- a/python/obitools3/parsers/universal.pyx +++ b/python/obitools3/parsers/universal.pyx @@ -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') diff --git a/python/obitools3/uri/decode.pyx b/python/obitools3/uri/decode.pyx index de8f11b..14dba86 100755 --- a/python/obitools3/uri/decode.pyx +++ b/python/obitools3/uri/decode.pyx @@ -10,6 +10,7 @@ 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 from obitools3.parsers.universal import entryIteratorFactory from obitools3.writers.fasta import FastaNucWriter @@ -478,6 +479,13 @@ def open_uri(uri, only=only) else: 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: raise NotImplementedError('Sequence file format not implemented') elif seqtype==b"prot":