[DAS] das stylesheets

[Andy Jenkinson]

I think the prevalence of this issue may come from the fact that 
ProServer's demo stylesheet has this instruction in it. I have updated 
the subversion repository to remove it.

Jonathan Warren wrote:
> 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.
> 
>