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

[Allan Kamau]

Hi Mark,
Thank you for your reply.
Calling setModeLazy() method of the object of type BlastLikeSAXParser 
did provide the cure.

Allan.

Mark Schreiber wrote:
> 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 
> <mailto: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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>