[Bioperl-l] Two Bio::DB::Flat swiss adaptors

Chris Fields cjfields at uiuc.edu
Wed Mar 21 18:31:45 EDT 2007


I think all secondary accessions are accessed via:

my @sec_acc = $seq->get_secondary_accessions();

At least that's what's in the test suite.

Go Illini!

chris

On Mar 21, 2007, at 5:02 PM, Seongwon "Terry" Seo wrote:

> I have a question regarding SwissProt.
> One ID can have multiple accessions in SwissProt, but I cannot find  
> where
> they are saved in Bioperl::Seq. Is there anyone can help me on this?
> Terry Seo.
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris  
> Fields
> Sent: Tuesday, March 20, 2007 11:34 PM
> To: Bioperl-L list
> Subject: [Bioperl-l] Two Bio::DB::Flat swiss adaptors
>
> Just curious, but why are there two Bio::DB::Flat::BDB swissprot
> adaptors (Bio::DB::Flat::BDB::swiss, Bio::DB::Flat::BDB::swissprot)?
> The only significant difference between the two is the following line
> in seq_to_ids():
>
> Bio::DB::Flat::BDB::swiss : $ids{VERSION}  = "$accession.$version"
> if defined $accession && defined $version;
> Bio::DB::Flat::BDB::swiss : $ids{VERSION}  = "$accession.version"
> if defined $accession && defined $version;
>
> The second is missing '$' in version, which I'm guessing is a bug?
>
> chris
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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