Hello -
MegaBLAST is not offcially supported. This doesn't mean it won't work it
just means we don't know if it will work. If it isn't too different from
normal blast it probably will.
The BlastLikeSAXParser has two modes. Lazy and Strict. If you call
setModeLazy() before parsing it won't care if it doesn't recognise the
format as one that is tried and tested and will attempt to parse it
anyway. You should carefully check a few results though to make sure it is
going well. If things work let us know so we can add MegaBLAST to the list
of trusted programs.
Hope this helps,
Mark
James Diggans <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
11/22/2004 02:38 PM
To: BioJava <[EMAIL PROTECTED]>
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Parsing MegaBLAST output files?
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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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