Hmm... looks like a genuine bug. I can't see anything immediately wrong in the source code and the blast results file looks normal too.
What I think has happened is that the BLASTP output format for multiple input query sequences has changed recently (I see you're using the March 2008 version) and the parser doesn't recognise this yet. If you have access to an older version of BLAST, could you try repeating your query with it and attempt to parse the output results to see if this theory is correct? Whatever happens, could you raise a bug at http://bugzilla.open-bio.org/ with the details and hopefully then someone else will be able to take a look at this some time this week (I'm away for the next few days now). cheers, Richard 2008/9/9 David Toomey <[EMAIL PROTECTED]>: > Hi Richard > > Thanks very much > > I was coding in netbeans so I have just included the source, I did split the > code up into a few separate classes but it is all directly from the > cookbook. This is in ie.rar and is kicked off from Main.java > The blast result file is also included in "test query.rar" > > The output I get when I run it is > > run: > Starting > databaseId : new_prot_target_for_download.fasta 4566 sequences; > 2,083,676 total letters > program : ncbi-blastp > queryLength : 284 > queryId : gi|5524211|gb|AAD44166.1| > version : 2.2.18 > Hits: > match: Cytochrome e score: 1.0E-108 > match: Cytochrome e score: 1.0E-13 > match: Cytochrome e score: 1.0E-9 > > > BUILD SUCCESSFUL (total time: 2 seconds) > > > Cheers > > Dave > > -----Original Message----- > From: Richard Holland [mailto:[EMAIL PROTECTED] > Sent: 09 September 2008 15:32 > To: David Toomey > Cc: biojava-l@lists.open-bio.org > Subject: Re: [Biojava-l] Parsing multiple query blast result > > Would it be possible for you to send the BLAST file and actual source > code you are working with? > > The list won't accept attachments, but you can send them directly to > me. If I can't fix it quickly or see anything obviously wrong with it, > I'll let you know ASAP so that you can post it back to the list for > someone else to investigate. (I'm going to be out at meetings for most > of the next 10 days so you probably don't want to wait for me to get > back!). > > cheers, > Richard > > 2008/9/9 David Toomey <[EMAIL PROTECTED]>: >> Hi >> >> >> >> I have been using the Blast Parser example in the cookbook and I have it >> working fine for a blast result with hits from a single query sequence. >> However when I attempt to process a file that contains blast results from > a >> search with multiple query sequences the ArrayList returned from the parse >> method only contains a single entry (from the first query sequence). Is >> there something I need to do to get the parser to return the results from >> all the query sequences. I am using Biojava 1.6. >> >> >> >> Thanks >> >> >> >> Dave >> >> >> >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l@lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -- > Richard Holland, BSc > Finance Director, Eagle Genomics Ltd > M: +44 7500 438846 | E: [EMAIL PROTECTED] > http://www.eaglegenomics.com/ > > -- Richard Holland, BSc Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: [EMAIL PROTECTED] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l
