[Biopython] codon-optimization method

[Peter Cock]

Hello Alex,

Yes, you can go ahead and make a pull request:

https://github.com/biopython/biopython/pull/4368

Depending on the nature of the change you have in mind, a little
disccusion before coding may make sense - especially if there is
more than one obvious way to tackle something.

It is also encouraging for us as maintainers if another user
on the mailing list (or via GitHub) shows support for some proposed
functionality (as we as individuals may not have a use for it).

Thanks,

Peter

On Thu, Jul 20, 2023 at 5:10 PM Alex Crocker <alex.w.crocker at gmail.com> wrote:
>
> Hello,
>
> I have added a method for codon optimization of a given sequence (DNA or protein) using the codon preferences contained in a CodonAdaptationIndex object.
>
> I created the method because existing fluorophore sequences were not functional in an organism I work with, and I wanted to quickly generate codon-optimized versions of the fluors for my organism.
>
> I included the method in biopython/Bio/SeqUtils/__init__.py, inside the CodonAdaptationIndex class. I also added a couple of lines in biopython/Tests/test_SeqUtils.py to apply the method to a sequence and assert that the calculated CAI after optimizing is equal to 1.
>
> I read the guidelines for contributing, but am not entirely clear on what I should do next. Would it be appropriate to go ahead and make a pull request?
>
> Thank you!
> Alex
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