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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