Another way to parse the results without using the full blown object model and SequenceDB is to extend SearchContentAdapter and listen for the events of interest. The event that gives you the query id is a callback to setQueryID(String id) on the adapter.
Take a look at http://www.biojava.org/docs/bj_in_anger/blastecho.htm for some hints. - Mark "Richard HOLLAND" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 11/11/2005 10:15 AM To: "Andreas Scheucher" <[EMAIL PROTECTED]>, <biojava-l@biojava.org> cc: (bcc: Mark Schreiber/GP/Novartis) Subject: RE: [Biojava-l] Extract accession number out of xml blast result As documented at BioJava in Anger, the subject's accession can be obtained from the SeqSimilaritySearchHit using getSubjectID(). By reading the API, the query's accession can be obtained from SeqSimilaritySearchResult using getQuerySequence().getName(). However... unforunately, the query accession method above does not work if you follow the BioJava in Anger example code! BlastLikeSearchBuilder requires a SequenceDB and a SequenceDBInstallation. The former should contain all sequences used in the query, and the latter should be able to provide SequenceDB instances corresponding to the databases used in the blast. For instance, if you blasted query "A12345" vs. database "nr", then the SequenceDB instance should return a meaningful value for getSequence("A12345"), and the SequenceDBInstallation instance should return a meaningful value for getSequenceDB("nr"). The example at BioJava in Anger uses a DummySequenceDB and DummySequenceDBInstallation to pass to the BlastLikeSearchBuilder. Both these instances generate the exact same response no matter what values you pass to getSequence() and getSequenceDB() - they return a Sequence or SequenceDB with the name of "dummy". If you are really interested in the actual query accession, you would need to provide your own SequenceDB which returned appropriately named sequences. If your queries all come from an existing SequenceDB object, you can just pass this straight in. Likewise, if you are really interested in the target database name, you can construct or use some other SequenceDBInstallation to provide the appropriate SequenceDB instances. BUT... you can get round all this object overkill by knowing a few things about your query data before trying to parse it. First, when you run BLAST on multiple query sequences in a single input file, the report generated will contain the query sequences in the same order as the input file. Second, the SeqSimilaritySearchResult objects are returned in the same order as the results appear in the BLAST report, and there will be one SeqSimilaritySearchResult object per query sequence. So, if you have a list of your query sequence accessions in the order they appear in the input file to BLAST, you can then maintain a counter which increments each time you obtain the next SeqSimilaritySearchResult, and that counter will provide a direct pointer into your list to tell you which query accession you are currently working with. Likewise, you should know already what blast database you blasted against, so you shouldn't really need to get this information from the results. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of > Andreas Scheucher > Sent: Thursday, November 10, 2005 6:49 PM > To: biojava-l@biojava.org > Subject: [Biojava-l] Extract accession number out of xml blast result > > > Hi, > > I'am parsing a blast result file for an multi fasta search > with biojava. > Now I'm wondering, whether there really is no possibility to get the > accession number out of an blast hit. The xml tag with the > information > is there but where ist the belonging function? > > Thanks for your effort. > > Regards, > Andreas > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
