def codons(self, genetic_code=SGC, codon_usage=_equal_codons):
"""Predicts most likely set of codon frequencies.
Optionally uses genetic_code (to figure out which codons belong
with each amino acid), and codon_usage (to get most likely codons for
each amino acid). Defaults are the standard genetic code and unbiased
codon frequencies.
"""
result = {}
normalized = Freqs(self)
normalized.normalize()
for aa, aa_freq in normalized.items():
curr_codons = genetic_code[aa]
if not curr_codons:
continue #code might be missing some amino acids?
curr_codon_freqs = Numbers([codon_usage[c] for c in curr_codons])
curr_codon_freqs.normalize()
for codon, c_freq in zip(curr_codons, curr_codon_freqs):
result[codon] = c_freq * aa_freq
return CodonUsage(result, self.info, genetic_code)
