This python script rebalances codon choices to avoid using codons that are rare in any of the desired species
Input format is currently hard coded and should be tab delimited file that looks like so:
- first row is header
- columns are Triplet, Amino Acid, Blank, Blank, Blank, Triplet, Fraction(yeast), Frequency(yeast), Number(yeast), Fraction(ecoli), Frequency(ecoli), Number(ecoli), Fraction(rice), Frequency(rice), Number(rice), Fraction(benthi), Frequency(benthi), Number(benthi)
Input arguments (in order)
- input table
- output name
- minimum fraction codon usage of other organism (not yeast) i.e. 0.1
- maximum fraction to remove of codon usage of yeast i.e. 0.3
Example usage
python3 ./rebalance_codon_usage.py codon_usage.tsv codon_usage_rebalanced.tsv 0.1 0.3