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

[Tobias Straub]

Scott, here you go, that's my conf file with the attribute('Name') 
labelling:

----------------- snip

[GENERAL]
description	= GFF3 test (memory)
db_adaptor	= Bio::DB::GFF
db_args		=	-adaptor memory
			-gff '/var/apache2/htdocs/gbrowse/databases/eden.gff'

stylesheet	= /gbrowse/gbrowse.css
buttons		= /gbrowse/images/buttons
tmpimages	= /gbrowse/tmp
help		= /gbrowse/

aggregators	= processed_transcript

default features = Gene

image widths  = 450 640 800 1024
default width = 800
stylesheet  = /gbrowse/gbrowse.css
buttons     = /gbrowse/images/buttons
tmpimages   = /gbrowse/tmp
max segment     = 50000
default segment = 5000
zoom levels    = 100 200 1000 2000 5000 10000 20000 40000 50000
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor      = beige

[TRACK DEFAULTS]
glyph         = generic
height        = 10
bgcolor       = lightgrey
fgcolor       = black
font2color    = blue
label density = 25
bump density  = 100
link          = AUTO

[Gene]
feature	= gene
glyph 	= transcript2
bgcolor = lightblue
label	= sub {
		my $f = shift;
		my @n = ($f->attributes('Name'), $f->attributes('Alias'));
		return $n[0];
	}
key	= gene	

[Transcripts]
feature		= processed_transcript
glyph		= processed_transcript
bgcolor		= peachpuff
label	= sub {
		my $f = shift;
		my @n = ($f->attributes('Name'));
		return $n[0];
	}
description	= 1
key		= Gene model


-----------snip -------------

the result is attached,

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Tobias

On 6 Jan 2006, at 17:52, Scott Cain wrote:

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