[Bioperl-l] RNAMotif parser

[Torsten Seemann]

Chris,

> I have been fiddling with an RNAMotif parser and an ERPIN parser for a
> number of years now; I plan on releasing it for inclusion in bioperl or
> bioperl-run.  Right now, I think I may base them somewhat on your
> Bio::Tools::QRNA module.  Should they be in bioperl (Bio::Tools::RNAMotif)
> or bioperl-run (Bio::Tools::Run::RNAMotif) namespace?

 From my understanding, a module to _parse the output_ of some TOOL goes 
in Bio::Tools::TOOL. The wrapper to _run_ TOOL goes in 
Bio::Tools::Run::TOOL. Usually the run() method in Bio::Tools::Run::TOOL 
takes the TOOL output and creates a Bio::Tools::TOOL object with the 
result in it as a convenience.

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/
Phone: +61 3 9905 9010