[Biojava-l] BlastXMLParserFacade

[Dan Bolser]

On Fri, 12 Mar 2004, Matthew Pocock wrote:

> Hi,
> 
> The parser shouldn't be throwing a NPE. However, the NCBI blast xml 
> output didn't used to be well-formed XML, so was not parseable by any 
> XML parser. I don't know if this has since been fixed by the NCBI.

! 


I have a perl module to 'clean up' large amounts of psi-blast data. Do
such modules exist in biojava?

Specifically, given a 'family' label for query database, I wanted a
'family' assignment to the target database, and my module did this by
assessing overlap within and between families. 

It would be really cool to do this a bit more systematically and
'modularly' with biojava.

 


> 
> Matthew
> 
> DMGoodstein at lbl.gov wrote:
> 
> >I was wondering if anyone has successfully gotten
> >BlastXMLParserFacade to work on an xml style NCBI
> >blast output file (version 2.2.3)? I'm getting null
> >pointer exceptions deep within the crimson parser
> >implementation classes, but I now i'm correctly
> >passing in the NCBI output file, since the dtd is
> >getting read.
> >
> >--David Goodstein
> >  Joint Genome Institute
> >
> >/usr/java/j2sdk1.4.1_02/bin/java2/bin/java
> >-classpath .:./biojava-1.3.1
> >.1.jar BlastParser fred.xml
> >a/j2sdk1.4.1_02/bin/javac -classpath .:./biojava-1.3.
> >java.lang.NullPointerException
> >	at
> >org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:524)
> >	at
> >org.apache.crimson.parser.Parser2.parse(Parser2.java:305)
> >	at
> >org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:442)
> >	at
> >org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.parse(BlastXMLParserFacade.java:172)
> >	at BlastParser.main(BlastParser.java:44)
> >1.jar BlastParser
> >./fred.xmlava/j2sdk1.4.1_02/bin/java -classpath
> >.:./biojava-1.3.1
> >java.lang.NullPointerException
> >	at
> >org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:524)
> >	at
> >org.apache.crimson.parser.Parser2.parse(Parser2.java:305)
> >	at
> >org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:442)
> >	at
> >org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.parse(BlastXMLParserFacade.java:172)
> >	at BlastParser.main(BlastParser.java:44)
> >
> >_______________________________________________
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> >
> >  
> >
> 
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