[Bioperl-l] RPSblast and existing BLAST packages (WAS: RemoteBlast)

[Richard Adams]

I'm not sure - here are some random musings
It seems easier to organize the modules by program package rather than
by program function - for example,
Smith-Waterman modules are distinct from Blast modules even though the
programs have similar aims. If we're going to have
a uniform access to Remote Blast and standalone blast then one way might
be to have BlastQuery class with common parameter
setting methods, and methods such as
   run_remote_blast
   run_local_blast
    which access the implementing code as appropriate. But this might be
a pain to implement without breaking everyone's existing code.

Or, since standaloneblast uses autoload
we could just add alternative allowable names for methods so that
$factory->p('blastn') and $factory->program('blastn')are treated the
same. Having method names the same as the header names in the blast URI
documentation might be best as I would suspect that everyone has used
the web interface but not everyone uses standalone blast.

Richard



--
Dr Richard Adams
Bioinformatician,
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams at ed.ac.uk