[Bioperl-l] GFF3 and Gbrowse

[Scott Cain]

Lincoln,

I hate to be a pain, but it is not in bioperl-live/Bio/DB/GFF/Aggregator
(updated just now).  Is it somewhere less obvious, or did you not cvs
add it?

Thanks,
Scott



On Tue, 2005-06-28 at 16:54 -0400, Lincoln Stein wrote:
> It's in bioperl CVS. A copy is also in the gbrowse CVS which will be installed 
> if it detects an old version of bioperl.
> 
> Lincoln
> 
> On Tuesday 28 June 2005 03:44 pm, Scott Cain wrote:
> > Lincoln,
> >
> > This is the first I've heard of the so_transcript aggregator; have you
> > committed it anywhere?
> >
> > Scott
> >
> > On Tue, 2005-06-28 at 13:24 -0400, Lincoln Stein wrote:
> > > The bioperl GFF database (both the inmemory and relational database
> > > versions) need to be brought up to date to handle the full expressive
> > > powerof GFF3. So for the time being ID trumps Name. Also you must use the
> > > so_transcript aggregator instead of the processed_transcript aggregator.
> > >
> > > Lincoln
> > >
> > > On Tuesday 28 June 2005 11:21 am, Andrew Nunberg wrote:
> > > > I was wondering if there is any documentation about using GFF3 format
> > > > with Gbrowse.  Since this is the "new" format, I wanted to start using
> > > > it, but observing some behaviors.
> > > >
> > > > The GFF3 documentation on http://song.sourceforge.net/gff3.shtml
> > > > indicates the Name tag is the id to be displayed and the ID tag is
> > > > unique and internal, however when I use Gbrowse 1.62 it is ID that is
> > > > being displayed as the label.
> > > >
> > > > I wish to use processed_transcript aggregator, the GFF3 document
> > > > indicates you only need to  display the exons and CDS and the UTRs will
> > > > be inferred, however I did not see that when  viewed in Gbrowse.
> > > >
> > > > If there is some extra code or documentation I need please let me know
> > > >
> > > > Thanks
> > > > Andy
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory