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.
Jonathan.
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
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
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Jonathan Warren
Senior Developer and DAS coordinator
[email protected]
Ext: 2314
Telephone: 01223 492314
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