Hi - Can you post the BLAST output that caused the problem?
- Mark On 9/4/07, Jianjun Wang <[EMAIL PROTECTED]> wrote: > > 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 > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
