[DAS] Insanity nearing, how stupid am I being!(Retrieve feature list from das ensembl)

[Thomas Down]

On Fri, May 31, 2002 at 09:58:07AM +0000, Oliver Lyttelton wrote:
> Hello,
>     Really simple one but I'm crawling up the wall on account of it! I can 
> retrieve features from the reference server using a url such as :-
> 
> http://servlet.sanger.ac.uk:8080/das/ensembl428/features?segment=X:10,50000
> 
> 
> but as soon as I try and get a list of features from an annotation server, 
> for example repeats from ens428rep, using a url like
> 
> http://servlet.sanger.ac.uk:8080/das/ens428rep/features?segment=X:10,58000
> 
> I get an empty xml document in return:-

That particular data source doesn't actually serve anything
in chromosomal coordinates.  However, if you fetch features from
an individual assembly contig it will work fine:

   http://servlet.sanger.ac.uk:8080/das/ens428rep/features?segment=AB019441.1.1.157090

A client should be able to discover the whole assembly structure
from the reference server -- there's a section on this in the DAS
specification.  If assembly-navigation doesn't appeal to you, there
are some toolkits which will take care of it for you: for example,
the DAS package in BioJava.

> Also, testing the urls in internet explorer 6 causes the browser to crash 
> approximately 50% of the time. (You've gotta love microsoft...)

*sigh* not a lot I can do to help here (other than to bingle
Mozilla a little bit).  However, I do find the simple command-line
`wget' tool very useful for testing purposes.

     Thomas.