[Biojava-l] parsing tblastn results

[David Toomey]

Hi Richard

This looks suspiciously like a bug I raised a couple of weeks ago. I was
parsing blastp results but the stack trace is the same.

http://bugzilla.open-bio.org/show_bug.cgi?id=2603

Charles, I have updated the original bug with a hack which at least allows
you to parse the result and get an output. You just need to recompile the
source code with the modified 'BlastLikeAlignmentSAXParser.java. Not ideal
but at least you will be able to run your code until the source is fixed.

Cheers

Dave

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Richard Holland
Sent: 15 October 2008 09:13
To: Charles Imbusch
Cc: biojava-l at biojava.org
Subject: Re: [Biojava-l] parsing tblastn results

I've raised a bug report for you. Hopefully someone will take a look at it
soon:

http://bugzilla.open-bio.org/show_bug.cgi?id=2617

cheers,
Richard

2008/10/14 Charles Imbusch <charles at imbusch.net>

> Hello,
>
> for a project I want to parse a tblastn result with BioJava. I used the
> code
> on http://biojava.org/wiki/BioJava:CookBook:Blast:Parser as it is and I
> get an
> error message as follows:
>
> Exception in thread "main" java.lang.StringIndexOutOfBoundsException:
> String index out of range: -3
>   at java.lang.String.substring(String.java:1938)
>   at java.lang.String.substring(String.java:1905)
>   at
>
org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.parseLine(BlastLikeA
lignmentSAXParser.java:289)
>   at
>
org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.parse(BlastLikeAlign
mentSAXParser.java:115)
>   at
>
org.biojava.bio.program.sax.HitSectionSAXParser.outputHSPInfo(HitSectionSAXP
arser.java:514)
>   at
>
org.biojava.bio.program.sax.HitSectionSAXParser.firstHSPEvent(HitSectionSAXP
arser.java:287)
>   at
>
org.biojava.bio.program.sax.HitSectionSAXParser.interpret(HitSectionSAXParse
r.java:251)
>   at
>
org.biojava.bio.program.sax.HitSectionSAXParser.parse(HitSectionSAXParser.ja
va:118)
>   at
>
org.biojava.bio.program.sax.BlastSAXParser.hitsSectionReached(BlastSAXParser
.java:635)
>   at
>
org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java:337
)
>   at
> org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:164)
>   at
>
org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXPars
er.java:313)
>   at
>
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.
java:276)
>   at
>
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java
:162)
>   at BlastEcho.echo(BlastEcho.java:29)
>   at BlastEcho.main(BlastEcho.java:75)
>
> I uploaded the Blast output file I want to parse here:
> http://charles.imbusch.net/tmp/blastresult.txt
>
> Any answer is appreciated.
>
> Cheers,
>  Charles
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/
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