[Bioperl-l] Primer3 Redux

Chris Fields cjfields at illinois.edu
Sun Apr 4 22:59:46 EDT 2010


On Apr 4, 2010, at 7:46 PM, Torsten Seemann wrote:

> Chris
> 
> I have been working on a Primer3 refactor (for $job) that is pretty much
>> ready to go; I'll be adding it to bioperl-dev in a few days along with
>> tests.  This'll also include a Primer3 wrapper.  It's a fairly major
>> overhaul, so I'm using
> 
> the namespace Bio::Tools::Primer3Redux in the meantime so there are no API
>> collisions (any other suggestions for a namespace are welcome).
>> 
> 
> This is fantastic!
> 
> I just wrote a bunch of primer3 2.x bioperl code, and when I ran it I
> realised bioperl-live only had 1.x support... although the SVN is down at
> the moment, I hope to test it soon when I can get access again.
> 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
> University, AUSTRALIA


Torsten,

I have committed the code to bioperl-dev.  It basically wraps primer3 (either 1.x or 2.x) and parses output.  I haven't added tests yet, but in some of my preliminary work it appeared to work just fine.  It's also possible I'll change the internals at some point to be less, um, hacky, but the API should remain the same.

I'll probably release it as a self-contained package to CPAN at some point.

chris


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