Great that is very helpful. One more question: Should I be using the Das1 or Das2 implementations. The demo I am looking at uses Das2 (I think), but I am running into problems. By modifying things in the Das2SourceHandler I can now get Ids (instead of using uri). Is this the right way of approaching this or should I be looking somewhere else..
When you say I have to play around with the URLs can you give me an example? Is the problem described above part of this? (this is not the URL but rather the XML..) Sorry for these questions, but I find it extremely difficult to get my head around all these different versions (DAS1/2; dasobert/programs.das; European/Rest;.) Thanks a lot, Bernd PS. I guess I should have attended the recent meeting. ;( _____ From: Jonathan Warren [mailto:[email protected]] Sent: Thursday, April 29, 2010 10:27 AM To: Bernd Jagla Cc: [email protected] Subject: Re: [Biojava-l] DAS client: how to retrieve features for a sequence region 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 _______________________________________________ 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. 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
