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

[Chris Fields]

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