Hi all, I've searched for a conclusive answer to the "Program ncbi-blastn Version <some value> is not supported" without success. I would like to know format of the blast output the Biojava's blast-like parsing framework likes, including some examples (without the data) of how such blast output may be created. For example, I am using ncbi-blastn and I am generating the blast file (which Biojava doesn't like) as follows.
export FORMATDB=/usr/local/share/blast/blast-2.2.17/bin/formatdb; export BLASTALL=/usr/local/share/blast/blast-2.2.17/bin/blastall; export REFERENCES_FASTA_NAME=/study/tmp/somesequence/blast/20071017.fasta; export BLAST_REPORT_TABULAR=somesequence.blast.txt export BLAST_REPORT_XML=somesequence.blast.xml export BLAST_REPORT=somesequence.blast export INPUT_FASTA=somesequence.fasta export WORK_DIR=/development/study/try1/tmpDataFiles/somesequence date;time cd $WORK_DIR;cp $REFERENCES_FASTA_NAME .;$FORMATDB -i $REFERENCES_FASTA_NAME -p F -o T;echo `pwd`;$BLASTALL -p blastn -d $REFERENCES_FASTA_NAME -i $INPUT_FASTA -q -1 -r 1 -m 8 -o $BLAST_REPORT_TABULAR;$BLASTALL -p blastn -d $REFERENCES_FASTA_NAME -i $INPUT_FASTA -q -1 -r 1 -m 7 -o $BLAST_REPORT_XML;date; Then I supply the $BLAST_REPORT as an argument to "BlastParser" copied from "http://biojava.org/wiki/BioJava:CookBook:Blast:Parser" Then I get the error below. [EMAIL PROTECTED] try1]$ $ANT_HOME/bin/ant runBlastParser; Buildfile: build.xml runBlastParser: [java] org.xml.sax.SAXException: Program ncbi-blastn Version 2.2.17 is not supported by the biojava blast-like parsing framework [java] at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:241) [java] at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160) Allan. _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l