[Bioperl-l] GFF3 and Gbrowse

[Lincoln Stein]

My memory is failing. The glyph and aggregator are named 
"processed_transcript"  I've also just now created a pair called 
"so_transcript" that do exactly the same thing. They should work with the 
GFF3 "canonical gene." Let me know if they don't.

Lincoln

On Tuesday 28 June 2005 04:54 pm, 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

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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Cold Spring Harbor, NY 11724
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