[Biojava-l] Problem with blast file parser

Andreas Prlic andreas at sdsc.edu
Thu Jan 29 21:11:51 UTC 2009


We had a couple of bug reports recently regarding issues that already
got fixed in the latest biojava builds from SVN. I think it is time to
start preparing the next biojava release ( 1.7 )  to make sure
everybody gets up to the latest status...


On Thu, Jan 29, 2009 at 12:55 PM, Marcel Huntemann
<marcel.huntemann at gmail.com> wrote:
> 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!
> Cheers,
> Marcel
> 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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