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

[Sheldon McKay]

I'm the guilty party.  We better hurry with the fix or the entire GFF2.5
user community (Mark) will start complaining.  I just found out today that
only flies and mosquitoes use the locus_tag qualifier, I've been neck deep
in game for too long.

Sheldon

----- Original Message -----
From: <lstein at cshl.edu>
To: <markw at illuminae.com>; <smckay at bcgsc.bc.ca>
Cc: <bioperl-l at bioperl.org>
Sent: Thursday, December 11, 2003 4:18 PM
Subject: Changes to GFF 2.5 "unflattening" code


> 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
>
> --
> Lincoln Stein
> lstein at cshl.edu
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
>