[Biojava-dev] biojava3 BLAST parser

[Scooter Willis]

Deniz

Can you provide some requirements regarding parsing the Blast XML. I tend to use XPATH and the DOM object to get to the data elements of interest so you already have the ability to load the Blast XML and work with the data. The difficulty of "parsing" is not an issue with XML. The BlastXMLQuery is an example of searching the Blast XML to get results. Are you wanting the XML elements translated to Java classes?

Thanks

Scooter

On Aug 31, 2010, at 2:46 AM, Deniz Koellhofer wrote:

> Hi,
> 
> I wanted to find out the current state of blast parsing efforts in biojava3
> - especially for ncbi blastxml output?
> 
> I had a quick look and found some DOM based code fragments
> in org.biojava3.genome.query.BlastXMLQuery. Is there already anybody working
> on a more comprehensive SAX parser?
> 
> The biojava1.7.1 blastxml parser seems to work fine, however some of the
> tags in NCBI-BLASTN 2.2.23+ output like Hsp_midline, BlastOutput_param don't
> seem to get parsed properly
> in org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.
> 
> Cheers,
> Deniz
> 
> -- 
> Deniz Koellhofer
> Cambia
> Initiative for Open Innovation (IOI)
> Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
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