[Bioperl-l] How to parse DBLINK Project linetype in Genbank file

[Mark A. Jensen]

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 at lanl.gov>
To: <Bioperl-l at lists.open-bio.org>
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.
>
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