[Biojava-l] DAS client: how to retrieve features for a sequence region

Jonathan Warren jw12 at sanger.ac.uk
Wed Apr 28 20:21:13 UTC 2010

Hi Bernd

For the UCSC you need to filter on types. see http://genome.ucsc.edu/FAQ/FAQdownloads.html#downloads 
  there is a section called "Downloading data from the UCSC DAS server"

for DAS libraries you can see a tutorial here http://www.biodas.org/wiki/DASWorkshop2010#Day_2

the one you would be most interested in is the Dasobert tutorial (http://www.ebi.ac.uk/~rafael/dokuwiki/doku.php?id=das:courses:dasobert 
) for DAS client creation, but there is a also a good javascript  
library as well called JSDas.

Any more info then don't hesitate to ask.


On 28 Apr 2010, at 08:25, Bernd Jagla wrote:

> Hi there,	
> I am trying to retrieve information (features) from the UCSC genome  
> browser
> using the DAS interface.
> I am looking at the org.biojava.bio.program.das sources. I can  
> retrieve all
> top level entry points with
> DASSequenceDB(dbURL)
> (Apperently the last entry from the return XML object gives a
> [Fatal Error] :1:1: Content is not allowed in prolog.
> Which I am ignoring...)
> and also the DSN entries using:
> DAS das = new DAS();
>    das.addDasURL(new URL(dbURLString));
>    for(Iterator i = das.getReferenceServers().iterator();  
> i.hasNext(); )
> {....
> When I try to access features for a top level entry point, i.e. a  
> reference
> sequence I have the impression that first all features for a given  
> reference
> sequence are being downloaded.
> My questions:
> How can I access only the features of a specific region? I guess in  
> terms I want to specify the segment part of the URL
> (http://genome.ucsc.edu/cgi-bin/das/hg17/features?segment=22:15000000,160000
> 00).
> I would also like to get the list of available features. How can I  
> achieve
> this? From a wireshark output I can see that this is being retrieved  
> somehow
> behind the scene. How can I access this information?
> I am looking at TestDAS*.java; are there any other examples around  
> that I
> can use to learn from?
> Thanks a lot for your kind support,
> Best,
> Bernd
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Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314

 The Wellcome Trust Sanger Institute is operated by Genome Research 
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