[Biojava-l] parsing tblastn results

[Richard Holland]

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(BlastLikeAlignmentSAXParser.java:289)
>   at
> org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.parse(BlastLikeAlignmentSAXParser.java:115)
>   at
> org.biojava.bio.program.sax.HitSectionSAXParser.outputHSPInfo(HitSectionSAXParser.java:514)
>   at
> org.biojava.bio.program.sax.HitSectionSAXParser.firstHSPEvent(HitSectionSAXParser.java:287)
>   at
> org.biojava.bio.program.sax.HitSectionSAXParser.interpret(HitSectionSAXParser.java:251)
>   at
> org.biojava.bio.program.sax.HitSectionSAXParser.parse(HitSectionSAXParser.java: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(BlastLikeSAXParser.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
> _______________________________________________
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> 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/