[Bioperl-l] 'virtual' seqs

[Lincoln Stein]

I am happy with an EmptySeq that returns undef because I already am paranoid 
and check for seq() returning undef (since Bio::DB::GFF::Segment can do 
this).

Lincoln

On Friday 28 June 2002 11:00 pm, Elia Stupka wrote:
> > IMHO the connotation of UnknownSequence is overloaded too (refering to
> > a sequence for which there is no functional annotation, or which
> > hasn't been characterized experimentally yet). It appears that
> > VirtualSeq has some consensus ... even though I recall someone (Elia?)
> > saying that's too overloaded either.
>
> I do think that VirtualSeq (not only in Ensembl) is often used to indicate
> a virtual *longer* sequence made by pulling together an assembly of
> sequences.
>
> The term Lazy really has to do with lazy fetching and nothing to do with
> an empty sequence.
>
> I still think EmptySeq is the simplest way to call something that we are
> all referring to as an empty sequence.... ;) but I don't really see why it
> should return NNNs... it is not meant to be storable with a sequence. In
> other words there is a good reason why EmptySeq->seq should return undef,
> and that is that it is not meant to be filled with a sequence, and thus
> no sequence is meant to be stored...
>
> I totally agree with Hilmar, we have tons of fully masked sequences, which
> are all made of NNNs... as well as gaps,etc. all made of NNNs, it really
> is not the same thing as an EmptySeq...
>
> Elia

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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