[Biojava-l] Parsing MegaBLAST output files?

[James Diggans]

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All, I'm attempting to use BioJava to parse the output from NCBI's
commandline MegaBLAST and receiving an error:

'Could not recognise the format of this file as one supported by the
framework.'

in a SAXException thrown by BlastLikeSAXParser. An old post to the
mailing list:

http://www.biojava.org/pipermail/biojava-dev/2002-October/000150.html

seems to indicate that this was fixed long ago via this commit to CVS:

http://cvs.biojava.org/cgi-bin/viewcvs/viewcvs.cgi/biojava-live/src/org/biojava/bio/program/ssbind/HeaderStAXHandler.java.diff?r1=1.3&r2=1.4&cvsroot=biojava

The MegaBLAST file I'm trying to parse is clean and my attempt at a
parse consists of (largely pulled from the recipe from BioJava in Anger):

- ------------------
InputStream is = new FileInputStream(blastResult);

BlastLikeSAXParser parser = new BlastLikeSAXParser();
SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
parser.setContentHandler(adapter);

alignmentResults = new ArrayList();
SearchContentHandler builder = new
	BlastLikeSearchBuilder(alignmentResults,
~                new DummySequenceDB("queries"),
		new DummySequenceDBInstallation());

adapter.setSearchContentHandler(builder);

parser.parse(new InputSource(is));
- ------------------

Any ideas on why I'm getting the SAXException? Thanks ...
- -j

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