Bioperl: Module collections...

[Steve A. Chervitz]

On Sat, 1 Aug 1998, Steven E. Brenner wrote:
> 
> Regarding BLAST,
> 
>    there are a fair number of modules around, and I should also note that
> I believe that a new, parsable output format will be released by NCBI
> before tooooo long.  We also will want to incorporate the ability to pass
> more flags to control PSI-BLAST. Furthermore, I think it is helpful to
> have the 'running' and the 'parsing' modules separate (with perhaps some
> wrapper module which does both).  So, I think it is premature to do too
> much with these modules.
 
Note that my module for running Blasts is separate from my parsing module
(Blast.pm). I have decided to make Blast.pm be essentially devoted to 
parsing and act as a wrapper for other Blast-related tasks. This makes  
it easier to use since you only need to remember "use Bio::Tools::Blast;" 
to get whichever functionality you need.

I explained this a little bit in:
http://genome-www.stanford.edu/perlOOP/bioperl/blast/Blast.pod.html#Module_Organization

SteveC
sac@genome.stanford.edu
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