[Bioperl-l] RNAMotif parser

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Sat Jan 28 05:04:30 EST 2006

>> 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.

> 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.  

I think this is still true. Anything in Bio::Tools::Run namespace should 
be in bioperl-run CVS (except for RemoteBlast and StandAloneBlast which 
are in bioperl-live core due to popularity). All the output parsers are 
in bioperl-live core.

Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
Phone: +61 3 9905 9010

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