[Biojava-l] Exception on Running BlastLikeSearchBuilder with null query SequenceDB

[Mark Schreiber]

Hi -

Can you post the BLAST output that caused the problem?

- Mark

On 9/4/07, Jianjun Wang <jwang at biohealthbase.org> wrote:
>
>  Oh, no, not PsiBlast. I'm using ncbi blastn. Thx.
> ________________________________
> From: Mark Schreiber [mailto:markjschreiber at gmail.com]
> To: Jianjun Wang [mailto:jwang at biohealthbase.org]
> Cc: biojava-l at lists.open-bio.org
> Sent: Tue, 04 Sep 2007 10:05:46 -0400
> Subject: Re: [Biojava-l] Exception on Running BlastLikeSearchBuilder with
> null query SequenceDB
>
>
> Hello -
>
>  Just out of interest what type of blast were you running. Some of the
>  more exotic forms like PSIBlast probably don't work well.
>
>  - Mark
>
>  On 9/4/07, Jianjun Wang <jwang at biohealthbase.org> wrote:
>  > Hi Colleagues,
>  >
>  > I used the Blast parsing example from the Biojava tutorial and ran into
> this problem:
>  > ######################
>  > Failed to build SeqSimilaritySearchResult:
>  > org.biojava.bio.BioException: Running BlastLikeSearchBuilder with null
> query SequenceDB
>  > at
> org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.makeSearchResult(BlastLikeSearchBuilder.java:239)
>  > at
> org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.endSearch(BlastLikeSearchBuilder.java:319)
>  > at
> org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter.endElement(SeqSimilarityStAXAdapter.java:119)
>  > at
> org.biojava.utils.stax.SAX2StAXAdaptor.endElement(SAX2StAXAdaptor.java:153)
>  > at
> org.biojava.bio.program.ssbind.SeqSimilarityAdapter.endElement(SeqSimilarityAdapter.java:136)
>  > at
> org.biojava.bio.program.sax.AbstractNativeAppSAXParser.endElement(AbstractNativeAppSAXParser.java:300)
>  > at
> org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:181)
>  > at
> org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:311)
>  > at
> org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:274)
>  > at
> org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160)
>  >
>  > ###########################
>  >
>  > I experimented with both supported Blast versions such as 2.2.3 and later
> ones, such as 2.2.13, and with the lazymode both on and off, and concluded
> that this problem is independent of Blast version and the lazymode. My
> debugging didn't yield much fruit, except that the obvious cause of the
> exception was BlastLikeSearchBuilder.querySeqHolder being
> null. Can someone shed some light on this?
>  >
>  > Here is the relevant section of my code:
>  >
>  > try {
>  > StringReader sr = new StringReader(in);
>  > BlastLikeSAXParser parser = new BlastLikeSAXParser();
>  > //works for 2.2.13?
>  > //parser.setModeLazy();
>  >
>  > //make the SAX event adapter that will pass events to a Handler.
>  > SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
>  >
>  > //set the parsers SAX event adapter
>  > parser.setContentHandler(adapter);
>  >
>  > //The list to hold the SeqSimilaritySearchResults
>  > //List results = new ArrayList();
>  >
>  > //create the SearchContentHandler that will build
> SeqSimilaritySearchResults
>  > //in the results List
>  > SearchContentHandler builder = new
> BlastLikeSearchBuilder(results);
>  >
>  > //register builder with adapter
>  > adapter.setSearchContentHandler(builder);
>  >
>  > //parse the file, after this the result List will be populated with
> SeqSimilaritySearchResults
>  > parser.parse(new InputSource(sr));
>  >
>  > //output some blast details - expect 1 result only
>  > ......
>  >
>  > Thanks,
>  > Jianjun
>  > _______________________________________________
>  > Biojava-l mailing list - Biojava-l at lists.open-bio.org
>  > http://lists.open-bio.org/mailman/listinfo/biojava-l
>  >
>