[Biojava-l] Problem with blast file parser

Marcel Huntemann marcel.huntemann at gmail.com
Thu Jan 29 20:55:15 UTC 2009

Hi Charles!

I've "found" a solution now. After dealing a couple of days with the
terrible xml output of blast and BioJava's BlastXMLParser (which also
wasn't working properly), I decided to have a look at the source code and
try to figure out myself what was wrong with the BlastLikeSAXParser. So I
 checked out the present status of the source code via the anonymous svn
checkout (howto here: http://biojava.org/wiki/CVS_to_SVN_Migration). After
a couple of hours and me not finding an error that could cause this
behavior, I thought I'll just give it a try and compiled the checked out
source via ant. Then used the new created biojava.jar and suddenly
everything went perfectly!
So, whatever the error was (unfortunately I don't have the old source code
to make a diff on certain files), it is already corrected in the
up-to-the-minute version in the subversion system.
Try it out!


Charles Imbusch wrote:
> Hello Marcel,
> I also do experience the problem that the parser is skipping
> the even result numbers. I have not found a sufficient solution
> for that, so I gave up on parsing on a blast result file containing
> multiple results. Instead I splitted up the big fasta file into
> serveral ones, so that I just get one result for one fasta file.
> That works, even it's not the best solution for it.
> Let me know if you find another solution for that problem.
> Cheers,
> Charles

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