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

[Chris Fields]

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 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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