cogent3.core.alphabet.KmerAlphabet

class KmerAlphabet(words: tuple[TStrOrBytes, ...], monomers: CharAlphabet[TStrOrBytes], k: int, gap: TStrOrBytes | None = None, missing: TStrOrBytes | None = None)

k-mer alphabet represents complete non-monomer alphabets

Attributes:

gap_char

gap_index

missing_char

missing_index

moltype

motif_len

num_canonical

Methods

count(value, /)	Return number of occurrences of value.
from_index(kmer_index)	decodes an integer into a k-mer
from_indices(kmer_indices[, independent_kmer])	converts array of k-mer indices into an array of monomer 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(seq[, validate])	encodes a k-mer as a single integer
to_indices(seq[, validate, independent_kmer])	returns a sequence of k-mer indices
to_json()	returns a serialisable string
to_rich_dict([for_pickle])	returns a serialisable dictionary
with_gap_motif([include_missing])	returns a new KmerAlphabet with the gap motif added

Notes

Differs from SenseCodonAlphabet case by representing all possible permutations of k-length of the provided monomer alphabet. More efficient mapping between integers and k-length strings