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

[Richard Holland]

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Sounds good to me.

Mark Schreiber wrote:
> Hi -
> 
> 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.
> 
> - Mark
> 
> 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.
>>
>> 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.
>>>     _______________________________________________
>>>     Biojava-l mailing list  -   Biojava-l at lists.open-bio.org
>>>     <mailto:Biojava-l at lists.open-bio.org>
>>
>>
>>>     http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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