Use Relevant Codon Frequency Data to Pull Codons for Primer Design

[David-Bianchi]

As a user, I would like to select the Codon mapping for each codon for that which has the highest RSCU for the relevant organism from: https://www.google.com/url?q=http://codonstatsdb.unr.edu/cgi-bin/submit.pl?species%3DEscherichia%2Bcoli%2B%2528taxid%253A%2B562%2529%26proteins%3DNuclear&sa=D&source=editors&ust=1757530875517525&usg=AOvVaw12GD47ng-qL0kRoApp3mcG

List of ACs:

AC1. Reads RSCU data from the resource given above (by downloading and reading the .tsv) - add the .tsv the /data in the repo.
AC2. Sorts by highest RSCU for each codon
AC3. Default, uses E. coli codon frequencies, given above
AC4. For the amino acid that is in mutation, selects the codon with the highest RSCU to be used in primer design, that replaces the following function called in design_primers(): https://github.com/Zhao-Group/Primer_Design_and_Worklists/blob/hardcode_to_args/Primer_Design_SDM.py#L129

In order to find the optimal codon (find_optimal_codon())

[David-Bianchi]

We can download the .tsv file from the site above, and then grab the codon with the highest RSCU using pandas etc. and sorting by RSCU in order to get the correct codon for design_primers().: https://github.com/Zhao-Group/Primer_Design_and_Worklists/blob/main/Primer_Design_SDM.py#L100

I already have some basic implementation of this in the open draft PR.

[David-Bianchi]

@David-Bianchi @avireusdev11 we'll need to replace: https://github.com/Zhao-Group/Primer_Design_and_Worklists/blob/hardcode_to_args/Primer_Design_SDM.py#L129

This method such that we select

For each amino acid, the codon with the highest RSCU.