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How to parse DBLINK Project linetype in Genbank file

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	How to parse DBLINK Project linetype in Genbank file by Chris Stubben :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message I have some Genbank files (from genome sequences) with a DBLINK line type listing the Entrez genome project id. Is there a way to parse this line? I can't seem to find it among the Annotation objects using bioperl 1.6.0 (printing all annotations or just dblinks below) my @annotations = $so->annotation->get_Annotations('dblink'); # nothing --- LOCUS NC_001664 159322 bp DNA linear VRL 16-OCT-2009 DEFINITION Human herpesvirus 6A, complete genome. ACCESSION NC_001664 VERSION NC_001664.2 GI:224020395 DBLINK Project:14462 KEYWORDS . SOURCE Human herpesvirus 6 (HHV-6A) Thanks, Chris Stubben
	Re: How to parse DBLINK Project linetype in Genbank file by Mark A. Jensen :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Chris-- This might be a bug; the HOWTO (at http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Getting_the_Annotations) states that the GenBank text is 'DBSOURCE'. Maybe we're not parsing the 'DBLINK' GenBank tag? A guru will surely chime in here. MAJ ----- Original Message ----- From: "Chris Stubben" <stubben@...> To: <Bioperl-l@...> Sent: Wednesday, October 21, 2009 11:29 AM Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file > > I have some Genbank files (from genome sequences) with a DBLINK line type > listing the Entrez genome project id. Is there a way to parse this line? > I can't seem to find it among the Annotation objects using bioperl 1.6.0 > (printing all annotations or just dblinks below) > > my @annotations = $so->annotation->get_Annotations('dblink'); # nothing > > --- > LOCUS NC_001664 159322 bp DNA linear VRL > 16-OCT-2009 > DEFINITION Human herpesvirus 6A, complete genome. > ACCESSION NC_001664 > VERSION NC_001664.2 GI:224020395 > DBLINK Project:14462 > KEYWORDS . > SOURCE Human herpesvirus 6 (HHV-6A) > > > Thanks, > > Chris Stubben > -- > View this message in context: > http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l
	Re: How to parse DBLINK Project linetype in Genbank file by Scott Markel :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Chris, Looking at the code for Bio::SeqIO::genbank dblink annotations are created for DBSOURCE lines, not for DBLINK lines. If you use your script on NP_042883, for example, you'll see a dblink annotation. A case-sensitive grep on DBLINK shows no matches in genbank.pm, so those lines don't currently lead to any annotations. Scott Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel@... Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Vice President, Board of Directors: International Society for Computational Biology Chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics -----Original Message----- From: bioperl-l-bounces@... [mailto:bioperl-l-bounces@...] On Behalf Of Chris Stubben Sent: Wednesday, 21 October 2009 8:29 AM To: Bioperl-l@... Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file I have some Genbank files (from genome sequences) with a DBLINK line type listing the Entrez genome project id. Is there a way to parse this line? I can't seem to find it among the Annotation objects using bioperl 1.6.0 (printing all annotations or just dblinks below) my @annotations = $so->annotation->get_Annotations('dblink'); # nothing --- LOCUS NC_001664 159322 bp DNA linear VRL 16-OCT-2009 DEFINITION Human herpesvirus 6A, complete genome. ACCESSION NC_001664 VERSION NC_001664.2 GI:224020395 DBLINK Project:14462 KEYWORDS . SOURCE Human herpesvirus 6 (HHV-6A) Thanks, Chris Stubben -- View this message in context: http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l
	Re: How to parse DBLINK Project linetype in Genbank file by Chris Fields-5 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message This should be parsed and available as Bio::Annotation::DBlink. I'll give it a check JIC. chris On Oct 21, 2009, at 11:06 AM, Mark A. Jensen wrote: > Chris-- This might be a bug; the HOWTO > (at http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Getting_the_Annotations > ) > states that the GenBank text is 'DBSOURCE'. Maybe we're not parsing > the 'DBLINK' GenBank tag? > A guru will surely chime in here. > MAJ > ----- Original Message ----- From: "Chris Stubben" <stubben@...> > To: <Bioperl-l@...> > Sent: Wednesday, October 21, 2009 11:29 AM > Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank > file > > >> >> I have some Genbank files (from genome sequences) with a DBLINK >> line type >> listing the Entrez genome project id. Is there a way to parse this >> line? >> I can't seem to find it among the Annotation objects using bioperl >> 1.6.0 >> (printing all annotations or just dblinks below) >> >> my @annotations = $so->annotation->get_Annotations('dblink'); # >> nothing >> >> --- >> LOCUS NC_001664 159322 bp DNA linear VRL >> 16-OCT-2009 >> DEFINITION Human herpesvirus 6A, complete genome. >> ACCESSION NC_001664 >> VERSION NC_001664.2 GI:224020395 >> DBLINK Project:14462 >> KEYWORDS . >> SOURCE Human herpesvirus 6 (HHV-6A) >> >> >> Thanks, >> >> Chris Stubben >> -- >> View this message in context: http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html >> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@... >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l
	Re: How to parse DBLINK Project linetype in Genbank file by Chris Fields-5 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Chris, Mark, Looks like it isn't parsed. I'll add a bug report to track, should be easy enough to add. Notably, gbdriver catches it but chokes b/c the type mapper is expecting a Bio::Annotation::DBlink (any non-specific information is by default pushed into a Bio::Annotation::SimpleValue, hence the painful death). chris On Oct 21, 2009, at 11:38 AM, Chris Fields wrote: > This should be parsed and available as Bio::Annotation::DBlink. > I'll give it a check JIC. > > chris > > On Oct 21, 2009, at 11:06 AM, Mark A. Jensen wrote: > >> Chris-- This might be a bug; the HOWTO >> (at http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Getting_the_Annotations >> ) >> states that the GenBank text is 'DBSOURCE'. Maybe we're not parsing >> the 'DBLINK' GenBank tag? >> A guru will surely chime in here. >> MAJ >> ----- Original Message ----- From: "Chris Stubben" <stubben@...> >> To: <Bioperl-l@...> >> Sent: Wednesday, October 21, 2009 11:29 AM >> Subject: [Bioperl-l] How to parse DBLINK Project linetype in >> Genbank file >> >> >>> >>> I have some Genbank files (from genome sequences) with a DBLINK >>> line type >>> listing the Entrez genome project id. Is there a way to parse >>> this line? >>> I can't seem to find it among the Annotation objects using bioperl >>> 1.6.0 >>> (printing all annotations or just dblinks below) >>> >>> my @annotations = $so->annotation->get_Annotations('dblink'); # >>> nothing >>> >>> --- >>> LOCUS NC_001664 159322 bp DNA linear VRL >>> 16-OCT-2009 >>> DEFINITION Human herpesvirus 6A, complete genome. >>> ACCESSION NC_001664 >>> VERSION NC_001664.2 GI:224020395 >>> DBLINK Project:14462 >>> KEYWORDS . >>> SOURCE Human herpesvirus 6 (HHV-6A) >>> >>> >>> Thanks, >>> >>> Chris Stubben >>> -- >>> View this message in context: http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html >>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@... >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@... >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l