[DAS] GBrowse as DAS server+Ensembl as DAS client

[Andy Jenkinson]

Hi Prem,

Each DAS coordinate system (e.g. GRCh_37 chromosomes) should always use the same sequence names between all DAS servers. In fact, compatibility between DAS servers is the primary reason for coordinate systems to exist. This allows all clients and servers to be sure that if they use the same coordinates then they can communicate with each other without having to know anything about each particular client/server. In truth the difference between the sequence names used by different genome browsers is a headache, and the net result is that coordinates are effectively defined by whoever uses them first (in this case being Ensembl). So, the GRCh37 coordinates use names like 1, 2, 3, X, MT as defined by Ensembl's reference server.

So gbrowse will need to detect this if it is to work properly, and also report a test_range without the "chr" prefix. As an aside, I believe UCSC (who also use the chrX format) do this conversion in their DAS server and can handle both formats.

Cheers,
Andy

On 7 Jan 2011, at 16:49, Prem Anand wrote:

> Hi
> 
> We are trying to set up our GBrowse as DAS server and were testing it with
> ensembl as client.
> 
> We have the right metadata in the datasource.conf file.
> 
> <COORDINATES uri="http://www.dasregistry.org/dasregistry/coordsys/CS_DS311"
> authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606"
> version="37" source="Chromosome">GRCh_37,Chromosome,Homo
> sapiens</COORDINATES>
> 
> The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) well.
> We also tried with different capabilities locally and it seems to be fine.
> 
> In all our GFF files/gbrowse databases we name the chromosomes prefexing
> with 'chr' as given in the test_range.
> 
> But ensembl client seems to ignore the test_range and is making the request
> as shown below ( from http access log)
> 
> /cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872
> HTTP/1.1" 200 345 "-" "Ensembl/60"
> 
> 
> And as GBrowse server doesn't recognise the region (1:114355433,114415381),
> it doesn't return anything back.
> In cgi-bin/das script, approximately at around line 860, if I prefix the
> $reference with 'chr', it works.
> 
> foreach (@segments) {
>        my ($reference,$refclass,$start,$stop) = @$_;
> 
>        if($reference !~ /^chr/){
>         $reference = "chr".$reference;
>        }
> 
> 
> We are not happy with this fix and wondering if it is a ensembl client issue
> or gbrowse server issue.
> 
> Shouldn't ensembl make the right request figuring out the right url from
> 'test_range'?
> OR
> If GBrowse server has to handle it in a better way?
> 
> Any directions would help.
> 
> Many Thanks
> Prem
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