SenseCodonAlphabet#

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

represents the sense-codons of a GeneticCode

Attributes:

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`(-> bool)	seq is valid for alphabet
`to_index`(codon)	encodes a codon as a single integer
`to_indices`(...)	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

from_indices(indices: ndarray[tuple[int, ...], 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

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

Return first index of value.

Raises ValueError if the value is not present.

to_rich_dict(for_pickle: bool = False) → dict#: returns a serialisable dictionary

with_gap_motif(**kwargs) → Self#

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

Notes

kwargs is for compatibility with the ABC method