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

[Chris Fields]

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 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.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l