Hi Allan - I think the solution is to call the setParserLazy() or some method with a similar name (I don't have the API handy). This will prevent it doing the check.
The original idea of this method was you could check against a list of version numbers that people had validated. I don't think this is a good idea as nothing is truely 100% validated and we haven't kept the list up to date. If there are no objections I would propose to make this method depricated (and it's opposite method) and change the default behaivour to lazy checking. Best regards. - Mark On 11/25/07, Allan Kamau <[EMAIL PROTECTED]> wrote: > > 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 - [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
