core.alphabet.SenseCodonAlphabet

core.alphabet.SenseCodonAlphabet(words, monomers, gap=None)

represents the sense-codons of a GeneticCode

Attributes

Name	Description
missing_char	not supported on CodonAlphabet
missing_index	not supported on CodonAlphabet
motif_len	always 3 for codon alphabets
num_canonical	returns the number of canonical states

Name	Description
from_index	returns a single codon from an index
from_indices	returns a list of codons from a numpy array of indices
from_rich_dict	returns an instance from a serialised dictionary
is_valid	seq is valid for alphabet
to_index	encodes a codon as a single integer
to_indices	returns a sequence of codon indices
to_json	returns a serialisable string
to_rich_dict	returns a serialisable dictionary
with_gap_motif	returns a new SenseCodonAlphabet with the gap motif ‘—’ added

core.alphabet.SenseCodonAlphabet.from_index(index)

returns a single codon from an index

core.alphabet.SenseCodonAlphabet.from_indices(indices)

returns a list of codons from a numpy array of indices

core.alphabet.SenseCodonAlphabet.from_rich_dict(data)

returns an instance from a serialised dictionary

core.alphabet.SenseCodonAlphabet.is_valid(seq)

seq is valid for alphabet

core.alphabet.SenseCodonAlphabet.to_index(codon, validate=True)

encodes a codon as a single integer

Name	Type	Description	Default
codon	str	string to be converted into index	required
validate	bool	raises an AlphabetError if the resulting sequence does not satisfy self.is_valid()	`True`

Name	Type	Description
	ValueError	if codon is not of length 3
	AlphabetError	if codon contains an invalid nucleotide or is not present in the code

core.alphabet.SenseCodonAlphabet.to_indices(seq, validate=True)

returns a sequence of codon indices

Name	Type	Description	Default
seq	str \| list[str] \| tuple[str, …] \| NumpyIntArrayType	input sequence to be converted to a numpy array of uint	required
validate	bool	raises an AlphabetError if the resulting sequence does not satisfy self.is_valid()	`True`

Name	Type	Description
	TypeError	if seq is unsupported type
	AlphabetError	if resulting sequence is not valid

core.alphabet.SenseCodonAlphabet.to_json()

returns a serialisable string

core.alphabet.SenseCodonAlphabet.to_rich_dict(for_pickle=False)

returns a serialisable dictionary

core.alphabet.SenseCodonAlphabet.with_gap_motif(**kwargs)

returns a new SenseCodonAlphabet with the gap motif ‘—’ added

kwargs is for compatibility with the ABC method