Re: Displaying top-level only of Multi-part features
Dear Timothy,
Many thanks, that glyph worked the way I wanted it to. Shame the arrow
one doesn't, but not to worry, I'm happy 
Thanks for the help guys.
Ellen
On 31/10/11 17:41, Timothy Parnell wrote:
> Hi Ellen,
>
> Have you tried looking at the box glyph? I use this for displaying genes
> in the region view when I don't need to see exon structure. From the
> description:
>
> This glyph draws genomic features as rectangles. If the feature
> contains subfeatures, then the glyph will draw a single solid box
> that
> spans all the subfeatures. Features can be named with a label at
> the
> top, and annotated with a descriptive string at the bottom.
>
> Tim
>
>
>
> On 10/31/11 9:41 AM, "Ellen Schofield"<ellen.schofield@...>
> wrote:
>
>> Hiya,
>>
>> Does anybody have anymore ideas please?
>>
>> Thanks,
>> Ellen.
>>
>> On 27/10/11 10:24, Ellen Schofield wrote:
>>> Hi Jason,
>>>
>>> Yes that is correct, please see the relevant snippet of our conf file
>>> below:-
>>>
>>> [GENE_MODEL_ENSEMBL:region]
>>> feature = gene:ensembl pseudogene:ensembl
>>> glyph = arrow
>>> key = Ensembl Predictions
>>> bgcolor = sub{
>>> my ($feature) = <at> _;
>>> return 'silver' if ($feature->primary_tag =~ /pseudogen/);
>>> return 'skyblue';
>>> }
>>> fgcolor = sub{
>>> my ($feature) = <at> _;
>>> return 'slategray' if ($feature->primary_tag =~ /pseudogen/);
>>> return 'steelblue';
>>> }
>>>
>>> Any other ideas?
>>>
>>> Cheers,
>>> Ellen
>>>
>>> On 26/10/11 23:08, Jason Stajich wrote:
>>>> And you are using this in your stanza?
>>>> feature=gene:SOURCE
>>>>
>>>> Jason
>>>> On Oct 26, 2011, at 1:50 AM, Ellen Schofield wrote:
>>>>
>>>>> Many thanks for the response Jason.
>>>>>
>>>>> I have tried using the arrow glyph, hoping that this didn't look at
>>>>> sub-parts. It correctly doesn't give the exon structure but still
>>>>> creates an arrow for ever transcript when I only want a single arrow
>>>>> for the gene (please see attached gbrowse_img as an example).
>>>>>
>>>>> Cheers,
>>>>> Ellen.
>>>>>
>>>>> On 25/10/11 19:35, Jason Stajich wrote:
>>>>>> you can use the 'arrow' glyph instead of transcript or gene glyph.
>>>>>>
>>>>>>
>>>>>> On Oct 25, 2011, at 9:14 AM, Ellen Schofield wrote:
>>>>>>
>>>>>>> Hi.
>>>>>>>
>>>>>>> We currently have gbrowse set up to display various features
>>>>>>> including
>>>>>>> some gene models. These show nicely with the correct hierachy of
>>>>>>> gene
>>>>>>> -> mRNA -> CDS. However, we would like to show just the gene
>>>>>>> spans (ie
>>>>>>> top level feature) in the region/overview sections of gbrowse, but
>>>>>>> it
>>>>>>> insists on showing the transcripts rather than the gene feature (I
>>>>>>> assume due to the code in Glyph.pm whereby it only draws the
>>>>>>> sub-parts).
>>>>>>>
>>>>>>> Is there a way to turn off the sub-parts if required? Or do we
>>>>>>> really
>>>>>>> have to load these feature in twice, once with the sub-features and
>>>>>>> once
>>>>>>> without as the code stands at the moment?
>>>>>>>
>>>>>>> Look forward to hearing from somebody.
>>>>>>>
>>>>>>> Yours,
>>>>>>> Ellen.
>>>>>>>
>>>>>>> --
>>>>>>> ellen.schofield@...
>>>>>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL)
>>>>>>> Cambridge Institute for Medical Research (CIMR)
>>>>>>> Wellcome Trust/MRC Building
>>>>>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
>>>>>>> Tel: 01223 763215
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>> _______________________________________________
>>>>>>> Gmod-gbrowse mailing list
>>>>>>> Gmod-gbrowse@...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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>>>>> --
>>>>> ellen.schofield@...
>>>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL)
>>>>> Cambridge Institute for Medical Research (CIMR)
>>>>> Wellcome Trust/MRC Building
>>>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
>>>>> Tel: 01223 763215
>>>>>
>>>>> <gbrowse_gene_features_arrow_glyph.png>
>> --
>> ellen.schofield@...
>> JDRF/WT Diabetes and Inflammation Laboratory (DIL)
>> Cambridge Institute for Medical Research (CIMR)
>> Wellcome Trust/MRC Building
>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
>> Tel: 01223 763215
>>
>>
>> --------------------------------------------------------------------------
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--
--
ellen.schofield@...
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215
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