[Bioperl-l] Bio::Tools::Primer3Redux released to CPAN

[Dave Messina]

Very cool, Chris! This will be a nice template for BioPerl Modules of the
Future.

Dave



On Mon, May 16, 2011 at 22:46, Chris Fields <cjfields at illinois.edu> wrote:

> All,
>
> Forgot to mention this on the list: I have released some code I had lying
> around (used in a local project) as Bio::Tools::Primer3Redux.  Grab it from
> CPAN if ya want it:
>
> http://search.cpan.org/dist/Bio-Tools-Primer3Redux/
>
> The main repo on github:
>
> https://github.com/cjfields/bio-tools-primer3redux
>
> == Features ==
>
> * Support for both primer3 v1 and v2.
> * The distribution contains both the wrapper
> (Bio::Tools::Run::Primer3Redux), the parser, and the related modules for
> storing data.  In other words, it's self-contained and not tied to a
> specific BioPerl version beyond some basic classes (Bio::Root::Root and
> Bio::SeqFeature::Generic).
> * Some Tests!
> * Some Documentation!
>
> == Why Primer3Redux? ==
>
> This is a rewrite of the BioPerl code for Primer3.  The key reason for a
> new name: the API differs significantly enough from the older Primer3 code
> to pretty much require a different namespace.  For some of the functionality
> I wanted at the time, the code pretty much required it (such as using
> hierarchal features).
>
> == Why not include this within BioPerl? ==
>
> Well, truthfully, I thought it would be a good idea to demonstrate that one
> can both (1) release BioPerl-reliant code on CPAN as a separate focused
> bundle and still contribute to BioPerl, and (2) use modern perl tools to do
> so (e.g. Dist::Zilla).  For more (and likely better) examples of the former,
> see: Bio::Graphics, Bio::DB::Sam, Bio::Chado::Schema, and numerous other
> modules.
>
> == To Do ==
>
> * Would probably be a good idea to genericize the base feature class being
> used so one could use any Bio::SeqFeatureI (e.g. Bio::DB::SeqFeature, for
> instance).
> * Separate the parser out; primer3 is still using Boulder format!
>
> == Thanks ==
>
> * Frank Schwach and Cass Johnston, for their input and bug reports.
> * UIUC
>
> chris
>
>
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