cogent3.core.alphabet.SenseCodonAlphabet

class SenseCodonAlphabet(words: tuple[str, ...], monomers: CharAlphabet[str], gap: str | None = None)

represents the sense-codons of a GeneticCode

Attributes:

gap_char

gap_index

missing_char

not supported on CodonAlphabet

missing_index

not supported on CodonAlphabet

moltype

motif_len

always 3 for codon alphabets

num_canonical

returns the number of canonical states

Methods

count(value, /)	Return number of occurrences of value.
from_index(index)	returns a single codon from an index
from_indices(indices)	returns a list of codons from a numpy array of indices
from_rich_dict(data)	returns an instance from a serialised dictionary
index(value[, start, stop])	Return first index of value.
is_valid(seq)	seq is valid for alphabet
to_index(codon[, validate])	encodes a codon as a single integer
to_indices(seq[, validate])	returns a sequence of codon indices
to_json()	returns a serialisable string
to_rich_dict([for_pickle])	returns a serialisable dictionary
with_gap_motif(**kwargs)	returns a new SenseCodonAlphabet with the gap motif '---' added