[Bioperl-l] [Bioperl-guts-l] [RFC] Module names (fwd)

[Jason Stajich]

John -

We use the namespace
Bio::Tools::Run
for anything which runs an external application.

All these modules are part of the bioperl-run CVS module (except
StandAloneBlast and RemoteBlast for historical reasons).  All the modules
inherit from Bio::Tools::Run::WrapperBase and have a defined set of
methods like 'program' and 'run' which allow us to have generic pluggable
modules in an analysis system.

For the record, there is already a Bio::Tools::Run::HMMPfam which
Shawn/Elia/Bala can comment on (er it does not use SearchIO as a parser
and in fact adds yet-another-parser, hope you guys know what you're doing
there).

In any event, if we could wrap your logic of a driver for running HMMER as
local binary (+/- pvm-enabled) and timelogic|paracel execution it would be
great.


-jason

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Mon, 10 Mar 2003 11:45:30 -0600
From: John A. Crow <crow at mail.ahc.umn.edu>
To: bioperl-guts-l at bioperl.org
Cc: crow at ccgb.umn.edu
Subject: [Bioperl-guts-l] [RFC] Module names


-- 

I would like to contribute a module to the Bioperl collection
and would be grateful for feedback/proposals for namespaces.

I suspect this module provides an alternative to existing
functionality in the current Bioperl collection, so please forgive
the redundancy if it exists.

At present, the module has the funky name

  XBio::HMMpfam

and "XBio" was selected as an interim name to avoid conflicts.
All it does is run hmmpfam. Associated with it are "drivers" that
specify the agent to do the actual execution. So maybe it's more
suggestive to show the directory structure:

  XBio
   |
   +-- HMMpfam.pm
   +-- HMMpfam
        |
        +-- decypher.pm     # Run on a TimeLogic Decypher box
        +-- local.pm        # Run a local binary

The "decypher.pm" and "local.pm" stuff is what I refer to as
"drivers" and certainly it would be possible to add other run
models. The basic use is like this:


   use XBio::HMMpfam;

   # Obtain a connection specifying the TimeLogic driver
   my $hmmpfam = XBio::HMMpfam->connect("decypher");

   # Set up an analysis
   my $analysis = $hmmpfam->analysis();
   $analysis->set_target('pfam');        # set the target to use

   # Run the analysis
   $analysis->execute($filename);
        .
        .
        .


So what I'd appreciate is feedback on better *names* to choose for
these modules. It will end up in CPAN so the fewer namespace collisions
the better I think.

Thanks -

 - John

_______________________________________________________________
John A. Crow
crow at ccgb.umn.edu

Center for Computational Genomics & Bioinformatics
University of Minnesota
Mayo MC 43
420 Delaware Street S.E.
Minneapolis, MN 55455 USA
http://ccgb.umn.edu/~crow
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