[Bioperl-l] GFF3 aggregation bottom-up

[Tobias Straub]

  Lincoln, (and whoever might be expert)

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?

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best
Tobias

======================================================================
Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany
======================================================================