[Bioperl-l] 'virtual' seqs
Thu, 20 Jun 2002 12:19:32 -0700
Grrr... outlook doesn't like interspersing comments in replies...
David Block firstname.lastname@example.org
GNF - San Diego, CA http://www.gnf.org
Genome Informatics / Enterprise Programming
> -----Original Message-----
> From: Jason Stajich [mailto:email@example.com]
> 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.
Apollo has the concept of a LazySeqI, where it is understood that the
sequence can be had for the asking, but it is lazily fetched. Would that
be a helpful interface here?
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 Stajich
> Duke University
> jason at cgt.mc.duke.edu
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