[Biojava-l] Blast parser

mark.schreiber at novartis.com mark.schreiber at novartis.com
Tue Jun 12 01:34:31 UTC 2007

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

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 
at org.biojava.bio.program.sax.BlastLikeSaxParser.parse 

Also, are there BioJava tools to process the xml output rather than the 
raw Blast output?

many thanks,

Dr S.L. Griffiths
Department of Chemistry
University of York
YO10 5YW

email: susy at ysbl.york.ac.uk
Tel. +44 (0)1904 328270
Fax +44 (0)1904 328266

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