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

Scott Markel SMarkel at accelrys.com
Wed Oct 21 12:26:29 EDT 2009


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 Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Stubben
Sent: Wednesday, 21 October 2009 8:29 AM
To: Bioperl-l at lists.open-bio.org
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
DEFINITION  Human herpesvirus 6A, complete genome.
VERSION     NC_001664.2  GI:224020395
DBLINK      Project:14462
SOURCE      Human herpesvirus 6 (HHV-6A)


Chris Stubben
View this message in context: http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html
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