[Bioperl-l] Re: Changes to GFF 2.5 "unflattening" code

[Scott Cain]

Lincoln and Sheldon,

For your information, I wrote a new genbank2gff3.pl script for use with
the pending GMOD release.  I anticipate that it will form the foundation
for rewriting the biofetch adaptor.  It uses Unflattener.pm and seems to
work for the organisms I tested (human, worm, fly, mosquito, and
Ecoli).  It is in the GMOD cvs in the schema repository at
schema/chado/load/bin/genbank2gff.PLS.

Scott

On Fri, 2003-12-12 at 10:56, bioperl-l-request at portal.open-bio.org
wrote:
> Hi Mark, Sheldon,
> 
> I saw your change to the _parse_gff2_group code in Bio::DB::GFF, which
> prioritizes "gene", "locus_tag" and "transcript" as group fields in
> the column 9 attributes.  I like it, but unfortunately it breaks some
> other code that I have, including the GMOD tutorial.
> 
> I think you'll like what I've done instead.  I've added a
> preferred_groups() method to which you pass a list of group names.
> Then, this list will be used as the priority list to pluck out groups
> from the GFF2 attribute list.  To get your previous behavior, you need
> to do this:
> 
>  $db = Bio::DB::GFF->new(-preferred_groups=>['gene','locus_tag','transcript'],
> 	                 @other_args);
>  $db->load_gff(...);
> 
> or this
> 
>  $db = Bio::DB::GFF->new(@other_args);
>  $db->preferred_groups('gene','locus_tag','transcript');
>  $db->load_gff(...);
> 
> You'll have to change your existing scripts accordingly.  Sure, this
> should be merged with Chris's unflattener, but then again let's just
> get to GFF3 as quickly as we possibly can and leave this nightmare
> behind us!
> 
> Lincoln
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory