[Biopython] codon-optimization method

[Alex Crocker]

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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