compiling Codon Optimizer on ubuntu 18.04

There is a cool old piece of software for codon optimization, inventively named "Codon Optimizer"

http://www.cs.ubc.ca/labs/beta/Projects/codon-optimizer/

It's not really very useful from a practical standpoint because its codon optimization strategy is to try to replace every codon with the highest CAI codon for the same amino acid. Which turns out to not be a very good strategy in practice. The software also can only optimize for E. coli, and has the translation tables and codon frequency tables hard-coded in.

Nevertheless, it's one of the few Open Source programs for codon optimization, so it might be useful to use as a starting point for a more fully-featured program, by adding more tables or some alternative algorithms for picking codons to use.

Unfortunately, it won't compile on Ubuntu 18.04.

To get it to compile, I had to do the following:

Codon translation tables in JSON format

I reformatted NCBIs genetic code tables (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=cgencodes) into JSON format.

Check out this link (http://www.petercollingridge.co.uk/tutorials/bioinformatics/codon-table/) for a quick algorithm for parsing these strings.

 codon_tables = {  
 "1": ["FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","---M------**--*----M---------------M----------------------------","Standard"],  
 "2": ["FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG","----------**--------------------MMMM----------**---M------------","Vertebrate Mitochondrial"],  
 "3": ["FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG","----------**----------------------MM----------------------------","Yeast Mitochondrial"],  
 "4": ["FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","--MM------**-------M------------MMMM---------------M------------","Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma"],  
 "5": ["FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG","---M------**--------------------MMMM---------------M------------","Invertebrate Mitochondrial"],  
 "6": ["FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","--------------*--------------------M----------------------------","Ciliate, Dasycladacean and Hexamita Nuclear"],  
 "9": ["FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG","----------**-----------------------M---------------M------------","Echinoderm and Flatworm Mitochondrial"],  
 "10":["FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","----------**-----------------------M----------------------------","Euplotid Nuclear"],  
 "11":["FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","---M------**--*----M------------MMMM---------------M------------","Bacterial, Archaeal and Plant Plastid"],  
 "12":["FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","----------**--*----M---------------M----------------------------","Alternative Yeast Nuclear"],  
 "13":["FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG","---M------**----------------------MM---------------M------------","Ascidian Mitochondrial"],  
 "14":["FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG","-----------*-----------------------M----------------------------","Alternative Flatworm Mitochondrial"],  
 "16":["FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","----------*---*--------------------M----------------------------","Chlorophycean Mitochondrial"],  
 "21":["FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG","----------**-----------------------M---------------M------------","Trematode Mitochondrial"],  
 "22":["FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","------*---*---*--------------------M----------------------------","Scenedesmus obliquus Mitochondrial"],  
 "23":["FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","--*-------**--*-----------------M--M---------------M------------","Thraustochytrium Mitochondrial"],  
 "24":["FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG","---M------**-------M---------------M---------------M------------","Pterobranchia Mitochondrial"],  
 "25":["FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","---M------**-----------------------M---------------M------------","Candidate Division SR1 and Gracilibacteria"],  
 "26":["FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","----------**--*----M---------------M----------------------------","Pachysolen tannophilus Nuclear"],  
 "27":["FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","--------------*--------------------M----------------------------","Karyorelict Nuclear"],  
 "28":["FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","----------**--*--------------------M----------------------------","Condylostoma Nuclear"],  
 "29":["FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","--------------*--------------------M----------------------------","Mesodinium Nuclear"],  
 "30":["FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","--------------*--------------------M----------------------------","Peritrich Nuclear"],  
 "31":["FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG","----------**-----------------------M----------------------------","Blastocrithidia Nuclear"]  
 }