Hi -
If you call parser.setModeLazy(); you will avoid the parser attempting to
check the version of blast. I
think lazy should be the default. I might submit a fix for this.
To parse XML into biojava objects you can use BlastXMLParser and
BlastXMLParserFacade. If you do this could you submit a recipe to the
cookbook as we don't have one for BlastXML yet.
Alternatively if you just want a single value from the BlastXML you could
probably just use an XPath compliant parser (XPath is supported in JDK1.5)
and get it that way.
- Mark
Susy Griffiths <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
06/11/2007 08:15 PM
Please respond to susy
To: [email protected]
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Blast parser
Hi,
I am trying to modify the BioJava cookbook example 'BlastParser' to
process output from a Blast search.
I get the following exception when I run this with the output I have
from the EBI web services NCBIBlast tool.
org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.15 is not
supported by the biojava blast-like parsing framework
at org.biojava.bio.program.sax.BlastLikeSaxParser.interpret
(BlastLikeSaxParser.java:241)
at org.biojava.bio.program.sax.BlastLikeSaxParser.parse
(BlastLikeSaxParser.java:160)
Also, are there BioJava tools to process the xml output rather than the
raw Blast output?
many thanks,
Susy
--
*********************************************************
Dr S.L. Griffiths
YSBL
Department of Chemistry
University of York
Heslington
York
YO10 5YW
UK
http://www.pims-lims.org/
email: [EMAIL PROTECTED]
Tel. +44 (0)1904 328270
Fax +44 (0)1904 328266
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