Hi Sean,
I've recently noticed a similar problem with some of my test databases.
Can you tell me what your are using on the backend?
Scott
On Tue, 2008-02-12 at 16:14 +0100, Sean O'Keeffe wrote:
> Hi all,
> I've just upgraded to 1.69 from 1.67 very successfully and compliments
> to all involved.
> My little gripe is the functionality of the gene.pm
>
> We've got a genes file containing no UTR or CDS (see below), just mRNA
> and exons.
> Setting 'sub_part = exon' worked a treat for displaying alternate exon
> structure in transcripts for 1.67
> I'm just getting one big generic block spanning the transcript in the
> new version
> I've included conf and a little of the file below.
>
> Sean.
>
>
> [Hs.hek]
> feature = gene:Solexa_subexons
> glyph = gene
> sub_part = exon # if no utr's or cds are in the file
> fgcolor = black
> bgcolor = dodgerblue
> height = 10
> label_transcripts = 1
> connector = 1
> pad_left = 50
> category = Genes
> linewidth = 1
> key = hek_hugues
> label = sub{
> my $feature = shift;
> my $label = join(' ', $feature->each_tag_value("Alias"));
> return $label;
> }
> description = 1
>
>
>
> ##gff-version 3
> chr20 Solexa_subexons gene 48984811 49008494 .
> - .
> ID=ENSG00000000419;ensembl_id=ENSG00000000419;Note=Total.count:135-Niter:262
> chr20 Solexa_subexons mRNA 48984811 49008494 .
> - .
> ID=ENST00000371584;Parent=ENSG00000000419;ensembl_id=ENST00000371584;Alias=0.104
> chr20 Solexa_subexons exon 48984811 48985180 .
> - . ID=ENST00000371584_E1;Parent=ENST00000371584
> chr20 Solexa_subexons exon 48986092 48986206 .
> - . ID=ENST00000371584_E2;Parent=ENST00000371584
> chr20 Solexa_subexons exon 48990809 48990877 .
> - . ID=ENST00000371584_E3;Parent=ENST00000371584
> chr20 Solexa_subexons exon 48991049 48991072 .
> - . ID=ENST00000371584_E4;Parent=ENST00000371584
> chr20 Solexa_subexons exon 48991073 48991153 .
> - . ID=ENST00000371584_E5;Parent=ENST00000371584
> chr20 Solexa_subexons exon 48991975 48992070 .
> - . ID=ENST00000371584_E6;Parent=ENST00000371584
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Gmod-gbrowse mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
--
------------------------------------------------------------------------
Scott Cain, Ph. D. [EMAIL PROTECTED]
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
Gmod-gbrowse mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
