[Bioperl-l] RNAMotif parser

Chris Fields cjfields at uiuc.edu
Fri Jan 27 20:47:48 EST 2006

Yeah, forgot about that.  I just remember a discussion at one point a while
back about splitting off sections of bioperl core b/c some thought
bioperl-core was getting too big; I didn't want to get too deep into writing
code w/o asking.  Okay, then, that's settled.  

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 
> -----Original Message-----
> From: Torsten Seemann [mailto:torsten.seemann at infotech.monash.edu.au]
> Sent: Friday, January 27, 2006 7:31 PM
> To: Chris Fields
> Cc: 'bioperl-ml List'
> Subject: Re: [Bioperl-l] RNAMotif parser
> 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

More information about the Bioperl-l mailing list