[ensembl-dev] Gene/transcript colour_key not loaded properly - SOLVED

[Ha X. Dang]

I just figured out if I remove 'key' => 'ensembl' from the web_data, the
colours show correctly.
This is probably that ensembl genes colour_key works differently.

Thanks.


//Ha


On Fri, Nov 5, 2010 at 2:15 PM, Ha X. Dang <dxha at vt.edu> wrote:

> Hi Ensemblers,
>
> I'm using Ensembl v56 and I have a genes predicted by several programs and
> want to color them differently in region view, so I add colour_key to the
> web_data field of the analysis corresponding to the gene predictor, eg. for
> geneid I have:
>
> analysis_description.web_data = {'colour_key' => 'geneid_gene', 'caption'
> => 'Genes','label_key' => '[text_label] [display_label]','name' =>
> 'Genes','default' => {'MultiTop' => 'gene_label','
> contigviewbottom' => 'transcript_label','MultiBottom' =>
> 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' =>
> 'as_collapsed_label','cytoview' => 'gene_label'},'key' => 'ensembl'}
>
> geneid_gene, gene_wise, etc. colour keys were already configured in
> COLOUR.ini file in [gene] section.
>
> Howerver, it doesn't seem to load the colour_key correctly for the gene
> object. I dumped the data and saw that for all genes/transcripts, the
> colour_key is always the same (eg. 'genewise_gene') and that made all
> genes/transcripts to have the same display color.
>
> Could someone have any idea on how this happens or point me to the module
> that load the web_data (colour_key) for gene/transcript object?
> Specifically, what is the module that loads:
>
>
> $gene->{my_config}{_tree_info}{nodes}{transcript_core_ensembl}{data}{colour_key}?
>
> I think there is some bug with this module.
>
> Thanks a lot.
>
>
> //Ha
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20101105/aa8a9a2e/attachment.html>