[Bioperl-l] RE: [Gmod-gbrowse] features not displaying

[Marc Logghe]

> 3) Bio::SeqFeature::Generic::get_tag_values does not exist 
> anymore: Bio::SeqFeature::Geneneric does not inherit from 
> Bio::AnnotatableI which implements that method, which is bad 
> (can it pass the tests, then ?). I don't know what the 
> situation is in bioperl-live HEAD.

Correction: get_tag_values is inherited from Bio::AnnotatableI via Bio::SeqFeatureI.

So, this error could be fixed by changing (in the 'horrible patch section' of package Bio::DB::Das::BioSQL bugfix-release)
*Bio::SeqFeature::Generic::attributes = \&Bio::SeqFeature::Generic::get_tag_values;
to:
*Bio::SeqFeature::Generic::attributes = \&Bio::AnnotatableI::get_tag_values; 

Making it even more horrible ;-)
But it works.
It seems that in older bioperl-live releases there actually *was* a Bio::SeqFeature::Generic::get_tag_values sub making the original hack work. In release 1.5.0 this sub was gone, breaking the hack.

Now, I'll try to tackle the double features problem. Status can be followed at
http://biologghe.homelinux.org:4380/cgi-bin/gbrowse/biosql?name=NP_491141%3A1..629;source=biosql;width=800;version=100;label=CDS-REGION-PROTEIN
(beware, it is a slow computer and a slow connection)

Cheers,
Marc