[Bioperl-l] Locuslink?? Help

[Eric Wang]

Thanks for your help!
Yeah, I noticed there isn't any top_features but
the annotations will contain reference sequence (NT_ contigs) ?
if that's the case, I would just use get_seq_by_id to retrieve it right?



Thanks again

Eric
On Wed, 14 May 2003, Hilmar Lapp wrote:

> my $seqio = Bio::SeqIO->new(-format => "locuslink");
> while(my $ll = $seqio->next_seq()) {
> 	# whatever
> }
> 
> There won't be any sequence features though. LL essentially is lots of 
> tag/value pairs, and that is how it ends up (i.e., 
> $ll->annotation->get_Annotations()).
> 
> The locus-contains-splice variants thing in LL isn't properly reflected 
> in the resulting SeqI object, which is a problem of the Bioperl object 
> model in the first place (there is no good object right now that would 
> properly reflect an LL object wrt the datatype). What you'd want is a 
> gene model. Maybe it's worth thinking whether the feature-driven 
> SeqFeature::Gene::* objects fit the bill here. I'm not convinced yet 
> though.
> 
> 	-hilmar
> 
> On Wednesday, May 14, 2003, at 05:44  PM, Eric Wang wrote:
> 
> > I have a question regarding how to retrieve locuslink objects.
> > I searched the documentation everywhere and couldn't find it.
> > Can anybody give me some pointers on how to retrieve locuslink objects 
> > and
> > can I use the top_Seqfeatures() for this object?
> >
> > Thanks in advance
> >
> > Eric
> >
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