[Biojava-l] parse (recent) blast output

[mark.schreiber at novartis.com]

Hello Dominique

It shouldn't be too hard to track down the problem. You might find the 
following program helpful in checking what the parser is up to when the 
error occurs. (http://www.biojava.org/docs/bj_in_anger/blastecho.htm), 
Using this along with stack traces and possibly a debugger you should be 
able to find out what is going wrong.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





Dominique Vlieghe <dominique.vlieghe at dmbr.ugent.be>
Sent by: biojava-l-bounces at portal.open-bio.org
08/22/2005 02:51 PM

 
        To:     Biojava <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] parse (recent) blast output


Hello fellow biojova'ers

I need, as every bioinformatician who uses java, a blast parser. I tried 
biojova's blastparser (from the cookbook), but recent blast outputs 
(2.2.10-11) are not supported. When I use the lazy method, I get a 
NullPointerException. So my questions are:

1) Has someone of you already succeeded in parsing these recent outputs?
2) Does anyone know why these outputs give me the exception? Has the 
output changed that much going from 2.2.3 to 2.2.10?
3) Would the software tweaks be difficult to implement? I have seen in 
the mailing list archives that some time ago there was a call to 
centralise the biojava parseblast enhancement efforts.  What is the 
status on that? I would like to contribute in (re)writing a blast 
parser, but only if it would serve the general community, so the biojava 
route would be preferred. But since I have outgrown the java newbie 
status only just and I'm totally new to biojava, any advice would be 
appreciated.

Cheers,

Dominique

==========
Exception in thread "main" java.lang.NullPointerException
   at 
org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java:215) 


   at 
org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:164)
   at 
org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:311) 


   at 
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:274) 


   at 
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160) 


   at BlastParser.main(BlastParser.java:44)

-- 
------------------------------------------------------------------------
Dominique Vlieghe, Ph.D.,
Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) 
VIB - Ghent University
Technologiepark 927 B-9052 Ghent (Zwijnaarde), Belgium
Tel : +32-(0)9-33-13.693          email: dominique.vlieghe at dmbr.ugent.be
Fax : +32-(0)9-33-13.609                www: http://bioit.dmbr.ugent.be/
------------------------------------------------------------------------

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