[Biojava-l] Blast parser

[mark.schreiber at novartis.com]

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 <susy at ysbl.york.ac.uk>
Sent by: biojava-l-bounces at lists.open-bio.org
06/11/2007 08:15 PM
Please respond to susy

 
        To:     biojava-l at lists.open-bio.org
        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: susy at ysbl.york.ac.uk
Tel. +44 (0)1904 328270
Fax +44 (0)1904 328266
*********************************************************

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