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 <[EMAIL PROTECTED]> 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 - [email protected]
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>
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