[Gmod-gbrowse] Re: [Bioperl-l] GFF3: preliminary or implemented?

[Lincoln Stein]

The idea of the ID is that it is just unique within the GFF3 file.  It does 
not necessarily translate into an ID for the feature itself.  I did some work 
on Bio::Tools::GFF so that it would deal with this correctly, but it hasn't 
been torture tested.  GBrowse handles the IDs correctly, but doesn't rely on 
Bio::Tools::GFF.

Lincoln


On Thursday 23 October 2003 12:48 pm, Chris Mungall wrote:
> It seems to me that we need to extend Bio::Tools::GFF to read/write the
> seqfeature nesting hierarchy using ID= and Parent= tags
>
> This seems a little problemmatic because it requires the notion of a
> unique id for features, which is lacking in bioperl
>
> How should we progress here? Should we add add a unique_id method to
> SeqFeature? Should this be autogenerated?
>
> On 23 Oct 2003, Charles Hauser wrote:
> > My last notes re:GFF3 were that it was in the 'preliminary' stage, but
> > it appears as though Jason update Tools::GFF to handle '='.
> >
> > Question: is GFF3 a supported version now & is  GBrowse happy w/ GFF3
> > formatting?
> >
> >
> > Charles
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
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-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
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