[Bioperl-l] which Primer3 module should we use now?

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Frank Schwach

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Mar 31, 2020, 9:28:10 AM3/31/20

to biop...@bioperl.org

Hi!

I have some old scripts that I wrote several years ago that use the module
Bio::Tools::Primer3Redux
to run primer3 and parse the results. But this hasn't been updated for
>2 years now and fails the tests with the latest version of primer3
(2.4.0).

The Bio::Tools::Primer3 module in BioPerl1.7.7 still seems to be limited
to primer3 versions 1.x which is now very much outdated.

What is the recommendation at the moment for running current versions of
primer3 from BioPerl?

Thanks!
Frank

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Fields, Christopher J

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Mar 31, 2020, 12:01:28 PM3/31/20

to Frank Schwach, biop...@bioperl.org

Hi Frank, it would be best to update Bio::Tools::Primer3Redux: https://github.com/cjfields/Bio-Tools-Primer3Redux. We should also add a deprecation for the modules in the main BioPerl distribution or simply split them out.

Would you be interested in adding support for this? I'm more than happy to add you to the repo. The Primer3 API has been a problem in keeping up with and I haven't used it in quite a while.