cogent3.core.genetic_code.GeneticCode

class GeneticCode(ID: int, name: str, ncbi_code_sequence: dataclasses.InitVar[str], ncbi_start_codon_map: dataclasses.InitVar[str], moltype: MolType[str] = MolType(('T', 'C', 'A', 'G')))

Holds codon to amino acid mapping, and vice versa.

Attributes:

sense_codons

start_codons

stop_codons

synonyms

Methods

get_alphabet(*[, include_gap, ...])	returns a codon alphabet
is_start(codon)	Returns True if codon is a start codon, False otherwise.
is_stop(codon)	Returns True if codon is a stop codon, False otherwise.
sixframes(seq)	Returns the six reading frames of the genetic code.
to_regex(seq)	returns a regex pattern with an amino acid expanded to its codon set
to_table()	returns aa to codon mapping as a cogent3 Table
translate(dna[, start, rc, incomplete_ok])	Translates DNA to protein.

Notes

We add additional states to the genetic code to represent gapped codons and missing data.