[Biojava-l] biojava BLAST parser proposal

[Simon Brocklehurst]

Peter Keller wrote:

> Hi Simon (and others),
>
> I am a little bemused by all this blast parser stuff. Blast output was
> never meant to be parsed, although lots of people try with varying
> degrees of success. However, the format of blast output files is not
> stable, and programs that parse them can break from time to time.

Peter,

We will continue to come up against software that we want to leverage, and that
provides problematic input and output (i.e. version- and option- specific etc.). We
have to deal with things as they *are*, but in a way that is as easy as possible to
maintain.

It would be great if everyone changed their software to emit well-designed XML.
Hopefully they will do that soon - which is why we're going for a SAX layer fairly
low down in the architecture.  At that point we can stop worrying about maintenance
of the lowest-level parsing layer.

Incidently, I see people starting to mention ASN.1 in incoming messages - we won't
be dealing with that, at least initially  (and possibly not ever!).

Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com