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

[Scott Cain]

Tobias,

I missed your second comment with regard to what look like 'extra'
features in your display.  Please send the track definition section that
you are using so I can take a look.

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