[DAS] Stylesheets and contigview

[Simon Twigger]

Thanks for filling me in, I just wanted to know if it was me doing  
something wrong or if Ensembl didnt use the stylesheets anyway.

It would be nice to be able to control the appearance a little bit, Im  
playing around with putting some non-standard annotations on there and  
its a little misleading to have it all look like a generic sequence  
feature. However, its not such a problem that I would want you to  
rearrange your to-do list.

Cheers,

	Simon

On Saturday, Dec 28, 2002, at 12:41 America/Chicago, Tony Cox wrote:

> Hi Simon,
>
> Ewan is right, Ensembl does not currently use (or even request) a  
> stylesheet
> from a remote DAS server. The resons are twofold. first it saves a bit  
> of
> time (although it would not be hard to cache it) and second it gives a
> little more control over the consistency of the contigview tracks. If  
> there
> were enough shouts for stylesheet support we could bump it up the list
> though.
>
> regards
>
> Tony
>
>> On Fri, 27 Dec 2002, Simon Twigger wrote:
>>
>>> Hi there,
>>>
>>> Taking my first personal foray into DAS, have the LDAS server working
>>> very nicely (Mac OS X 10.2) and I've been playing around with some  
>>> rat
>>> annotations viewed on the Ensembl contigview. I tried setting a style
>>> sheet as described in the LDAS installation manual (which was great,
>>> very easy to follow) and it doesnt seem to be having any effect on  
>>> how
>>> things appear on the contigview display.
>>
>> Simon - Great that you have got this working. This is wonderful news.  
>> I
>> suspect that Ensembl does not honour all the stylesheet hints (I  
>> think DAS
>> clients are allowed to do this). Tony Cox (cc'd in here) is the  
>> person who
>> really knows what is happening.
>>
>>
>>>
>>> Sample .das annotations:
>>>
>>> [annotations]
>>> SSLP D2Rat239 microsatellite epcr 1 16662 16847 . . .
>>> SSLP D2Rat381 microsatellite epcr 1 72253 72498 . . .
>>> SSLP D1Rat245 microsatellite epcr 1 1571523 1571694 . . .
>>>
>>> Style sheet:
>>>
>>> [microsatellite]
>>> glyph = primers
>>> bgcolor = black
>>> fgcolor = red
>>> height = 6
>>> bump = 1
>>>
>>> Ignoring the fact that microsatellites thought to be on Chr2 are
>>> appearing on chromosome 1 when we run ePCR, will this combination of
>>> annotation and style sheet work to give me the primer glyph on
>>> contigview? Everything displays as a box glyph (I presume this is the
>>> default) and the color seems to be whatever I set in the 'Manage
>>> Sources' options on the contigview.
>>>
>>> I noticed that the description of style sheets in the LDAS page is  
>>> very
>>> GBrowse-like whereas the official stylesheet documentation
>>> (http://www.biodas.org/documents/spec.html) referred to on the LDAS
>>> page is full blown XML - do both of these work, should I use one  
>>> rather
>>> than the other?
>>>
>>> Any advice would be most appreciated.
>>>
>>> Cheers,
>>>
>>> Simon.
>>>
>>>
>>> --------------------------------------------------------------------- 
>>> ---
>>> --------------------------
>>> Simon Twigger, Ph.D.
>>> Assistant Professor, Bioinformatics Research Center
>>>
>>> Medical College of Wisconsin
>>> 8701 Watertown Plank Road,
>>> Milwaukee, WI, 53226
>>> tel. 414-456-8802, fax 414-456-6595
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS@biodas.org
>>> http://biodas.org/mailman/listinfo/das
>>>
>>
>> -----------------------------------------------------------------
>> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
>> <birney@ebi.ac.uk>.
>> -----------------------------------------------------------------
>>
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>
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------------------------------------------------------------------------ 
--------------------------
Simon Twigger, Ph.D.
Assistant Professor, Bioinformatics Research Center

Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, 53226
tel. 414-456-8802, fax 414-456-6595