[BioPython] wu-blast 2.0 standalone parser?

[Brad Chapman]

Hi Ralf;

> are there any efforts to build a pythonic parser for the licensed 
> version of wahington university wu-blast 2.0 standalone?
> should this be done using the event based martel parser architecture?

These is some initial effort -- Andrew wrote a wu-blast grammar for
Martel, which you can find in Bio/expressions/blast/wublast.py.
There is no "Biopython-like" framework built up around that yet,
however, just the grammar.

> is there a martel - based parser for ncbi blast?

Yes, there is also Martel code for NCBI blast in the same directory
-- Bio/expressions/blast/ncbiblast.py
The Bio.Blast code does not use Martel currently -- at some time in
the future I'd like to see it integrated, if only to keep the
ncbiblast.py code up to date and to speed up parsing.

> slightly off topic - does it still make sense to support both wu and 
> ncbi blast?

Sure, we are happy to support whatever format people are still
using. As with anything, it just takes someone willing to put the
time into producing and maintaining a quality parser.

Hope this helps.
Brad