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 <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
08/22/2005 02:51 PM
To: Biojava <biojava-l@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: [EMAIL PROTECTED]
Fax : +32-(0)9-33-13.609 www: http://bioit.dmbr.ugent.be/
------------------------------------------------------------------------
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