[Bioperl-l] 'virtual' seqs

[Jason Stajich]

On Wed, 26 Jun 2002, Hilmar Lapp wrote:

> I like LazySeq best -- it means the absence of the sequence is not
> written in stone, fetching is just expensive and can take a while.
>
> Also, one should be able to write these sequences to transport the
> annotation and feature table (without potentially expensive sequence
> transport, too). In this case a parser's write_seq() method asking the
> object for the sequence should get an empty string instead of
> triggering the actual sequence fetch. At least as an option.
>
> I'm wondering how this should be implemented ... not sure what's the
> right thing to do.
>

I think for LazySeqs (which would be implicitly fetchable) we would
require a db handle ( Bio::DB::SeqI handle) to be available when it is
initialized.  Lincoln's Bio::DB::GFF::RelSegment is one implementation
that should fit the bill - it does more for coordinate mapping that I
think we would need for a simple proxy object.  I'll see about specing out
an interface I guess - things are piling up though so I'm not sure how
soon I can get to this after all.  I'd be very happy for someone else to
take an interest and try and support a better representation of GAME
objects in bioperl, otherwise I'll get to it at some point.

> 	-hilmar
>
> > -----Original Message-----
> > From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> > Sent: Thursday, June 20, 2002 11:57 AM
> > To: Bioperl
> > Subject: [Bioperl-l] 'virtual' seqs
> >
> >
> > We are processing datafiles - bsml,game, (agave?) documents
> > where it is
> > possible to just know the length of the sequence but not have
> > any actual
> > sequence data associated.  I think we should have sequence
> > objects which
> > can handle this - they would have a length, but seq() would warn and
> > return undef.  We need one that would implement Bio::Seq::RichSeqI
> > interface - call it VirtualRichSeq ? Perhaps we'll need the equivalent
> > PrimaryVirtualSeq and VirtualSeq?
> >
> > Can someone think of a better name, I don't want to confuse
> > with Ensembl
> > VirtualXX objects?  This would be implemeted in Bio::Seq:: namespace.
> >
> > -jason
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu