[Bioperl-l] Re: BLAST parsers

[Neil Saunders]

Ewan wrote:
> But for the moment the 1.0 series is the stable series, and there one does
> have a choice of three BLAST parsers, with (in my view) BPlite currently
> the stablest and most robust.
> There is where we should point users with the caveat that we think
> Bio::SearchIO is the way of the future.

I think the BLAST parsing situation is getting a little confusing.  I
also prefer BPlite and have many scripts based around it.  There are
also 2 versions floating around IIRC; one spelt BPLite (large L), the
other BPlite (small l).  One of these supports the 'multi' method (parse
reports with multiple query sequences), the other doesn't.  I generally
find myself downloading BPlite.pm from Ian Korf's page each time I do a
bioperl upgrade and copying it to the correct path.  And despite
upgrading to the latest bioperl pretty much as it's released, I'm barely
aware of Bio::SearchIO, which I guess is the old documentation problem.

After all, our aim is that no-one should have to write a BLAST parser
again!  I think updating the documentation is an important step here, to
avoid newbie confusion.

Neil
-- 
School of Biotechnology and Biomolecular Sciences,         
The University of New South Wales,                          
Sydney 2052,                                               
Australia                                                  
                                                            
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