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 > > [EMAIL PROTECTED] 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) > > > >_______________________________________________ > >Biojava-l mailing list - [EMAIL PROTECTED] > >http://biojava.org/mailman/listinfo/biojava-l > > > > > > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
