[DAS] Stylesheets and contigview

[Ewan Birney]

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>. 
-----------------------------------------------------------------