The link I gave you http://www.ebi.ac.uk/~rafael/dokuwiki/doku.php?id=das:courses:dasobert
shows examples of how to connect to 'European' style das sources.
For the UCSC and GBrowse type DAS sources you may have to play around
with the urls to get the info you want as they work slightly
differently to other DAS data sources and use the types to filter
data. I would suggest contacting the UCSC for more info.
The dasobert library is what you should use- the DASSequenceDB.java
that you are currently looking at in biojava are old and not really
supported anymore.
I was hoping to be able to use most of the functionality especially
for the parsing of the XML and creating the URLs by means of
functions/methods that are already around…
this is what the dasobert library is for ;)
On 29 Apr 2010, at 07:30, Bernd Jagla wrote:
Hi Jonathan,
Just to clarify, I need to write my own das client? I was hoping to
be able to use most of the functionality especially for the parsing
of the XML and creating the URLs by means of functions/methods that
are already around…
I am now going into debug mode for the DAS package in biojava to
look for the XML parsing, if you any further pointers on specific
methods I should be looking at it would mean a lot to me…
In short, I think I can create the URLs from scratch with not much
effort. I don’t currently know how to put the XML into a data
structure and how this data structure should look like.
Thanks for your kind help,
Bernd
From: Jonathan Warren [mailto:[email protected]]
Sent: Wednesday, April 28, 2010 10:21 PM
To: Bernd Jagla
Cc: [email protected]
Subject: Re: [Biojava-l] DAS client: how to retrieve features for a
sequence region
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
-- The Wellcome Trust Sanger Institute is operated by Genome
Research Limited, a charity registered in England with number
1021457 and a company registered in England with number 2742969,
whose registered office is 215 Euston Road, London, NW1 2BE.
Jonathan Warren
Senior Developer and DAS coordinator
[email protected]
Ext: 2314
Telephone: 01223 492314
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
_______________________________________________
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