[DAS] das stylesheets

[Jonathan Warren]

Warning!

please note that if you are setting up a das server with a stylesheet,  
be sure to not have <BUMP>0</BUMP> as strange things happen in clients  
such as ensembl- remove these tags if you're not sure what to do with  
them!

Thanks

Jonathan

See issue below posted to ensembl dev list:

Abel Ureta-Vidal wrote:
>
> Hi,
>
> This is maybe more for the DAS/Web team. I'm interested in  
> structural variation data (CNV, chromosome gain/loss, etc....)
> I've identified some data in Ensembl that is integrated via DAS  
> sources. I've identified the original DAS sources and
> query them directly, no problem, they work as expected.
>
> I'd just like to report a couple of things on the Ensembl web  
> display side of things.
>
> 1/The live ensembl server points to 2 DAS sources for CNVs from  
> Redon et al paper (Nature 2006 I presume),
> i.e. WGTP_loci_36 and WGTP_regions_36.
> I could not find a clear description of the exact difference between  
> the 2, (what does WGTP stands for? Whole Genome
> Tiling Platform?). Querying them directly and looking at their data,  
> it seems that these are 2 identical data sets
>
> $ GET http://das.sanger.ac.uk/das/WGTP_loci_36/features?segment=5:17198060,18198059 
>  > WGTP_loci_36
> $ GET http://das.sanger.ac.uk/das/WGTP_regions_36/features?segment=5:17198060,18198059 
>  > WGTP_regions_36
> $ diff WGTP_loci_36 WGTP_regions_36
> 5c5
> <   <GFF version="1.01" href="http://das.sanger.ac.uk:80/das/WGTP_loci_36/features 
> ">
> ---
> >   <GFF version="1.01" href="http://das.sanger.ac.uk:80/das/WGTP_regions_36/features 
> ">
>
> If I query the complete data from chromosome 5, I get exactly the  
> same **none** difference. These 2 sources
> seem to be identical. Only WGTP_regions_36 is listed and validate in  
> the DAS registry (www.dasregistry.org). Should
> this one only be considered as the reference?
>
> On the short region I queried 5:17198060,18198059, 5 features come  
> back. But I can only see 4 in the Ensembl Detailed View
> FEATURE id="Chr5tp-4G10:Gain=32|loss=39" label="Chr5tp-4G10:Gain=32| 
> loss=39"
> START 17417700
> END 17583657
> seems to be missing.
> All features have different ids so this is not a feature grouping  
> artifact I presume.
>
> 2/ Same kind of issue with decipher and decipher_collapsed_36  
> sources. Only decipher is in the DAS registry.
>
> $ GET http://das.sanger.ac.uk/das/decipher/features?segment=5:16621834,16821833 
>  > decipher
> $ GET http://das.sanger.ac.uk/das/decipher_collapsed_36/features?segment=5:16621834,16821833 
>  > decipher_collapsed
> $ diff decipher decipher_collapsed
> 5c5
> <   <GFF version="1.01" href="http://das.sanger.ac.uk:80/das/decipher/features 
> ">
> ---
> >   <GFF version="1.01" href="http://das.sanger.ac.uk:80/das/decipher_collapsed_36/features 
> ">
>
> Here 4 features are returned but only 1 displayed.
>
> So am I missing something? or these sources are data duplications.  
> And is there a display problem?

This is an identified issue - the DAS sources in both cases say DO NOT  
BUMP - so we don't hence we cannot display all the features. We have  
solved this for some sources by getting them to remove the "<BUMP>0</ 
BUMP>" entries in the stylesheets.


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