[Bioperl-l] 'virtual' seqs

[Elia Stupka]

> For the issue of returning undef vs. a string of characters, why not
> parameterize the behavior during creation of the object? That is:
> 
> my $vs = Bio::Seq::VirtualSequence->new( -len => 5000, -pad => "X");

I like this, stops our discussion and makes us all happy, I think.

Elia


> 
> ...would generate a seq string corresponging to ("X" x 5000). If not
> defined, then seq() would be left as undef. This has the advantage of
> allowing the user to specify another character (such as "N", or even
> "." or "-") as the placeholder character. Disadvantage when the user
> sets something REALLY odd, like "7" or "fruit fly", and that causes
> complaints later. At some point I guess you have to trust the user to
> be moderately kind to the API.
> 
> I have no feelings about the name of such an object...
> 
> -Charles
> 
> Lincoln Stein wrote:
> > 
> > I think it's important that we be able to perform manipulations on feature
> > tables and annotations even when the underlying sequence is completely
> > unavailable (not even a guarantee that you can fetch the sequence if you wait
> > long enough).  Laziness is a great feature, but it's more of an
> > implementation issue than something that should be exposed to the API.
> > 
> > As Ewan suggests, it's probably better to return a string of N's rather than
> > an undef sequence; otherwise lots of programs will break.  However I think
> > that EmptySequence has the wrong connotation.  I prefer VirtualSequence, or
> > possibly UnknownSequence.
> > 
> > Lincoln
> > 
> > On Wednesday 26 June 2002 06:59 pm, 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.
> > >
> > >       -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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> > > > Bioperl-l@bioperl.org
> > > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
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> > 
> > --
> > ========================================================================
> > Lincoln D. Stein                           Cold Spring Harbor Laboratory
> > lstein@cshl.org                                   Cold Spring Harbor, NY
> > ========================================================================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> 
> 

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