[Bioperl-l] Re: [Gmod-gbrowse] GFF3 aggregation bottom-up

[Scott Cain]

Hi Tobias,

What you are seeing is a result of some of the shoe-horning that had to
be done to make GFF3 fit into the current GFF schema.  These problems
will go away when Lincoln is done working on the new GFF3 schema.  Until
then, you can get the labels right by using a simple callback in the
track configuration, like this:

label       = sub {
                    my $feature = shift;
                    my ($name)  = $feature->attributes('Name');
                    return $name;
                  }

Scott

On Fri, 2006-01-06 at 15:06 +0100, Tobias Straub wrote:
> Lincoln,
> 
> On my way to get the gadfly gff3 files displayed properly I was trying  
> to rebuild the canonical gene (EDEN) that you describe in your GFF3  
> summary on song.sourceforge.net.
> Using bioperl 1.5.1  
> (http://bioperl.org/DIST/current_core_unstable.tar.gz) and gbrowse I  
> can neither get just 3 properly processed_transcript features nor the  
> proper names (i.e. EDEN.1, EDEN.2, EDEN.3) for those when using the  
> following GFF3 file (as in-memory or mysql database).
> 
> ##
> ##gff-version 3								
> ##sequence-region	ctg123	1	1497228					
> ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;Name=EDEN
> ctg123	.	TF_binding_site	1000	1012	.	+	.	ID=tfbs00001;Parent=gene00001
> ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001;Name=EDEN.1
> ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001;Name=EDEN.2
> ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA00003;Parent=gene00001;Name=EDEN.3
> ctg123	.	exon	1300	1500	.	+	.	ID=exon00001;Parent=mRNA00003
> ctg123	.	exon	1050	1500	.	+	.	ID=exon00002;Parent=mRNA00001,mRNA00002
> ctg123	.	exon	3000	3902	.	+	.	ID=exon00003;Parent=mRNA00001,mRNA00003
> ctg123	.	exon	5000	5500	.	+	.	ID=exon00004; 
> Parent=mRNA00001,mRNA00002,mRNA00003
> ctg123	.	exon	7000	9000	.	+	.	ID=exon00005; 
> Parent=mRNA00001,mRNA00002,mRNA00003
> ctg123	.	CDS	1201	1500	.	+	0	ID=cds000001;Parent=mRNA0001; 
> Name=edenprotein.1
> ctg123	.	CDS	3000	3902	.	+	0	ID=cds000001;Parent=mRNA0001; 
> Name=edenprotein.1
> ctg123	.	CDS	5000	5500	.	+	0	ID=cds000001;Parent=mRNA0001; 
> Name=edenprotein.1
> ctg123	.	CDS	7000	7600	.	+	0	ID=cds000001;Parent=mRNA0001; 
> Name=edenprotein.1
> ctg123	.	CDS	1201	1500	.	+	0	ID=cds000002;Parent=mRNA0002; 
> Name=edenprotein.2
> ctg123	.	CDS	5000	5500	.	+	0	ID=cds000002;Parent=mRNA0002; 
> Name=edenprotein.2
> ctg123	.	CDS	7000	7600	.	+	0	ID=cds000002;Parent=mRNA0002; 
> Name=edenprotein.2
> ctg123	.	CDS	3301	3902	.	+	0	ID=cds00003;Parent=mRNA0003; 
> Name=edenprotein.3
> ctg123	.	CDS	5000	5500	.	+	1	ID=cds00003;Parent=mRNA0003; 
> Name=edenprotein.3
> ctg123	.	CDS	7000	7600	.	+	1	ID=cds00003;Parent=mRNA0003; 
> Name=edenprotein.3
> ctg123	.	CDS	3391	3902	.	+	0	ID=cds00004;Parent=mRNA0003; 
> Name=edenprotein.4
> ctg123	.	CDS	5000	5500	.	+	1	ID=cds00004;Parent=mRNA0003; 
> Name=edenprotein.4
> ctg123	.	CDS	7000	7600	.	+	1	ID=cds00004;Parent=mRNA0003; 
> Name=edenprotein.4
> ##
> 
> 
> please find attached the gbrowse out put when using processed_trancript  
> aggregator and processed trancsript glyph.
> Is that behaviour expected?
> 
> 
> best
> Tobias
> 
> ======================================================================
> Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
> tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany
> ======================================================================
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory