Oh, no, not PsiBlast. I'm using ncbi blastn. Thx.
_____
From: Mark Schreiber [mailto:[EMAIL PROTECTED]
To: Jianjun Wang [mailto:[EMAIL PROTECTED]
Cc: [email protected]
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 <[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]
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
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