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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Richard Holland Sent: 15 October 2008 09:13 To: Charles Imbusch Cc: [EMAIL PROTECTED] 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 <[EMAIL PROTECTED]> > 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 - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: [EMAIL PROTECTED] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
