[Biojava-l] Bug in WuBlastSummaryLineHelper.java

[Simon Brocklehurst]

Matthew Muller wrote:

> I am using WU-BLAST version 2.0MP and am had some trouble using
> BlastLikeSaxParser to parse the output.  A NoSuchElement exception is
> thrown from WuBlastSummaryLineHelper and I think I've figured out
> why.  The exception occurs because the class tries to parse out the
> reading frame from the summary line output of blastx.  My version of
> blastx (2.0MP) does not print a reading frame and I don't see how any
> version should.  I think this is a bug.

Hi Matt,

First, I assume you're using the parser in lazy mode, because the
particular version of wu-blast you're using isn't supported by the
framework.  If you aren't using the parser in lazy mode, I'd like to
know, because the system should detect that this version isn't supported
and throw an exception.

Second, if you look in the biojava distribution at
demos/files/wublast/blastx.out - which is a sample output from file from
wu-blastx - you will see that the version of wu-blast currently support
by the framework (2.0a19MP-WashU) *does* appear to print out a reading
frame in the summary line.

So as far as I can see right now, this isn't a bug.

I think the right way to handle this situation is to add support for the
version of wu-blast you're using (yes I know the documentation for doing
this is poor/non-existent).   I am trying to put together some
documentation for doing this, but the best I can say is that it will be
done when it's done ;-)

Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com