[Biojava-l] error: Program ncbi-blastn Version 2.2.17 is not supported

[Mark Schreiber]

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 <allank at sanbi.ac.za> 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 $BLAST_REPORT as an argument to "BlastParser" copied
> from "http://biojava.org/wiki/BioJava:CookBook:Blast:Parser"
>
> Then I get the error below.
>
>
> [aaron at localhost try1]$ $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.
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