[Biojava-dev] biojava3 BLAST parser

[Deniz Koellhofer]

*Hi Scooter,*
*
*
*Thanks for the reply. I guess the BlastXMLQuery is a good example to show
how to quickly extract information from a BLAST result. *
*
*
*But in my opinion biojava3 should alo have a Blast parser that generates
java beans containing the complete Blast result set - similar to what
biojava1.7.1 was doing. So yeah, I'm after translating the XML elements to
Java classes.*
*
*
*Would something like that fit into one of the biojava3 modules? homology,
I/O?*
*
*
*Thanks,*
*Deniz*
*
*
On Tue, Aug 31, 2010 at 8:43 PM, Scooter Willis <HWillis at scripps.edu> wrote:

> 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
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>


-- 
-- 
Deniz Koellhofer
Cambia
Initiative for Open Innovation (IOI)
Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia