[Bioperl-l] RichSeqI

[Jason Stajich]

On Tue, 30 Jan 2001, Ewan Birney wrote:

> 
> To prove to hilmar that I am doing the RichSeqI stuff, I have committed
> the interface. Basically this is a trivial recasting of the "additional 
> support" currently in Seq.pm which I will move out into
> Bio::Seq::RichSeq.pm
> 
> 
> currently the interface looks like...
> 
> 
> =head1 NAME
> 
> Bio::Seq::RichSeqI - RichSeq interface, mainly for database orientated
> sequences
> 
> =head1 SYNOPSIS
> 
>     @secondary   = $richseq->get_secondary_accessions;
>     $division    = $richseq->division;
>     $mol         = $richseq->molecule;
>     @dates       = $richseq->get_dates; 
>     $seq_version = $richseq->seq_version;  
>        
> 
> =head1 DESCRIPTION
> 
> This interface extends the Bio::SeqI interface to give additional
> functionality to sequences with richer data sources, in particular from
> database sequences (EMBL, GenBank and Swissprot).
> 
> 
> Kris, Jason, Hilmar --- comments?

We have static set of methods for handling the fields you describe above
as well as a set of dynamic methods (via AUTOLOAD) to deal with things
like PID (bug #160), genbankid.  Or does most of that get wrapped into
secondard_accessions?  I guess are there any other fields we are missing?


> 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/