cogent3.core.alphabet.CharAlphabet#

class CharAlphabet(chars: TStrOrBytes | PySeq[TStrOrBytes], gap: TStrOrBytes | None = None, missing: TStrOrBytes | None = None)#

representing fundamental monomer character sets.

Attributes:

Methods

`array_to_bytes`(seq)	returns seq as a byte string
`as_bytes`()	returns self as a byte string
`convert_seq_array_to`(*, alphabet, seq[, ...])	converts a numpy array with indices from self to other
`count`(value, /)	Return number of occurrences of value.
`from_indices`(seq)	returns a string from a sequence of indices
`from_rich_dict`(data)	returns an instance from a serialised dictionary
`get_kmer_alphabet`(k[, include_gap])	returns kmer alphabet with words of size k
`get_subset`(motif_subset[, excluded])	Returns a new Alphabet object containing a subset of motifs in self.
`index`(value[, start, stop])	Return first index of value.
`is_valid`(seq)	seq is valid for alphabet
`to_indices`(seq[, validate])	returns a sequence of indices for the characters in seq
`to_json`()	returns a serialisable string
`to_rich_dict`([for_pickle])	returns a serialisable dictionary
`with_gap_motif`([gap_char, missing_char, ...])	returns new monomer alphabet with gap and missing characters added

Notes

Provides methods for efficient conversion between characters and integers from fundamental types of strings, bytes and numpy arrays.