[Bioperl-l] 'virtual' seqs

[Hilmar Lapp]

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.

	-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
> 
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