[Biojava-dev] biojava3 BLAST parser

[Deniz Koellhofer]

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