[Bioperl-l] Locuslink?? Help

[Hilmar Lapp]

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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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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