Hardcoded variables to CLI

[David-Bianchi]

Pull Request for Command Line Interface (CLI-version), that has accessible and default arguments (matching the examples) for main python file.

`usage: Primer_Design_SDM.py [-h] [-m MUTATION_LIST] [-o OUTPUT_DIRECTORY] [-f PRIMER_OUTPUT_FILE] [-fwd FORWARD_PRIMERS_FILE]
[-rev REVERSE_PRIMERS_FILE] [-c NCBI_CODON_TABLE_VALUE] [-orf ORF_FILE]

optional arguments:
-h, --help show this help message and exit
-m MUTATION_LIST, --Mutation_List MUTATION_LIST
List of Mutation Names mapped to well positions
-o OUTPUT_DIRECTORY, --Output_Directory OUTPUT_DIRECTORY
Output directory
-f PRIMER_OUTPUT_FILE, --Primer_Output_File PRIMER_OUTPUT_FILE
Output file for primers assoc. characteristic data
-fwd FORWARD_PRIMERS_FILE, --Forward_Primers_File FORWARD_PRIMERS_FILE
Output file for Forward primers
-rev REVERSE_PRIMERS_FILE, --Reverse_Primers_File REVERSE_PRIMERS_FILE
Output file for Reverse primers
-c NCBI_CODON_TABLE_VALUE, --NCBI_Codon_Table_Value NCBI_CODON_TABLE_VALUE
NCBI Codon Translation Table ID Value
-orf ORF_FILE, --ORF_File ORF_FILE
File containing Open Reading Frame Sequence`

I will make a fork to a DEV (development) branch so that we are not pushing to main, and such that the main branch is stable.

Also includes:

• requirements.txt - updated Python versions (including updated Biopython modules for Tm/GC calculation)

• Initial Translation Table via command line args. (for any NCBI Translation table: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi). To do: Add codon frequency tables.

To Test: IN PROGRESS adding further tests

#Test CLI arguments:
python Primer_Design_SDM.py -h

#Test on default arguments (example files):
python Primer_Design_SDM.py

#Test using a different translation codon table:
python Primer_Design_SDM.py -c NUM

Where NUM equals the INT value for the NCBI ID from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
for which you would like to update/use the genetic code from.

[David-Bianchi]

Switched base branch to "dev" development branch.

[David-Bianchi]

Testing: IN PROGRESS adding further tests

1. Test CLI arguments:
   python Primer_Design_SDM.py -h

2. Test on default arguments (example files):
   python Primer_Design_SDM.py

3. Test using a different translation codon table:
   python Primer_Design_SDM.py -c NUM

Where NUM equals the INT value for the NCBI ID from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
for which you would like to update/use the genetic code from.

[David-Bianchi]

Add codon frequency implementation with: https://pypi.org/project/python-codon-tables/

EDIT: Actually we will use the process and dataset described here: https://docs.google.com/presentation/d/1izx4LNw9vPYZ9hdI4wG6X0JyfeMrFNmBsP01yGkc4cs/edit?slide=id.g37d47b63948_0_6#slide=id.g37d47b63948_0_6

and in the associated comments on this slide, by selecting the codon with the highest sorted RSCU - this is described in the following issue: #2