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

[Bernd Jagla]

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 DAS
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