[Biojava-l] error: Program ncbi-blastn Version 2.2.17 is not supported
markjschreiber at gmail.com
Tue Nov 27 03:16:35 UTC 2007
Does anyone mind if I change the default behaivor to lazy parsing?
Technically this would be a break in backwards compatibility (although
only if you have a program that relies on strict parsing).
Last chance to complain.
On Nov 26, 2007 8:02 PM, Allan Kamau <allank at sanbi.ac.za> wrote:
> Hi Mark,
> Thank you for your reply.
> Calling setModeLazy() method of the object of type BlastLikeSAXParser
> did provide the cure.
> 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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> > <mailto:Biojava-l at lists.open-bio.org>
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