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

count(value, /)#: Return number of occurrences of value.

from_index(index: int) → str#: returns a single codon from an index

from_indices(indices: ndarray[tuple[Any, ...], dtype[integer]]) → list[str]#: returns a list of codons from a numpy array of indices

classmethod from_rich_dict(data: dict[str, Any]) → SenseCodonAlphabet#: returns an instance from a serialised dictionary

property gap_char: str | None#

property gap_index: int | None#

index(value, start=0, stop=sys.maxsize, /)#

Return first index of value.

Raises ValueError if the value is not present.

is_valid(seq: str | bytes | ndarray[tuple[Any, ...], dtype[integer]]) → bool#: seq is valid for alphabet

property missing_char: None#: not supported on CodonAlphabet

property missing_index: None#: not supported on CodonAlphabet

property moltype: MolType[StrOrBytes] | None#

property motif_len: int#: always 3 for codon alphabets

property num_canonical: int#: returns the number of canonical states

to_index(codon: str, validate: bool = True) → int#

encodes a codon as a single integer

Parameters:

codon: string to be converted into index
validate: raises an AlphabetError if the resulting sequence does not satisfy self.is_valid()

Raises:

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

to_indices(seq: str | list[str] | tuple[str, ...] | ndarray[tuple[Any, ...], dtype[integer]], validate: bool = True) → ndarray[tuple[Any, ...], dtype[integer]]#

returns a sequence of codon indices

Parameters:

seq: input sequence to be converted to a numpy array of uint
validate: raises an AlphabetError if the resulting sequence does not satisfy self.is_valid()

Raises:

TypeError: if seq is unsupported type
AlphabetError: if resulting sequence is not valid

to_json() → str#: returns a serialisable string

to_rich_dict(for_pickle: bool = False) → dict[str, Any]#: returns a serialisable dictionary

with_gap_motif(**kwargs: Any) → Self#

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

Notes

kwargs is for compatibility with the ABC method