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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l 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. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
