core.alphabet.CharAlphabet

core.alphabet.CharAlphabet(chars, gap=None, missing=None)

representing fundamental monomer character sets.

Notes

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

Name	Description
array_to_bytes	returns seq as a byte string
as_bytes	returns self as a byte string
convert_seq_array_to	converts a numpy array with indices from self to other
from_indices	returns a string from a sequence of indices
from_rich_dict	returns an instance from a serialised dictionary
get_kmer_alphabet	returns kmer alphabet with words of size k
get_subset	Returns a new Alphabet object containing a subset of motifs in self.
is_valid	seq is valid for alphabet
to_indices	returns a sequence of indices for the characters in seq
to_json	returns a serialisable string
to_rich_dict	returns a serialisable dictionary
with_gap_motif	returns new monomer alphabet with gap and missing characters added

core.alphabet.CharAlphabet.array_to_bytes(seq)

returns seq as a byte string

core.alphabet.CharAlphabet.as_bytes()

returns self as a byte string

core.alphabet.CharAlphabet.convert_seq_array_to(alphabet, seq, check_valid=True)

converts a numpy array with indices from self to other

Name	Type	Description	Default
alphabet	CharAlphabet[Any]	alphabet to convert to	required
seq	NumpyIntArrayType	ndarray of uint8 integers	required
check_valid	bool	validates both input and out sequences are valid for self and other respectively. Validation failure raises an AlphabetError.	`True`

Name	Type	Description
	the indices of characters in common between self and other
	are swapped

core.alphabet.CharAlphabet.from_indices(seq)

returns a string from a sequence of indices

core.alphabet.CharAlphabet.from_rich_dict(data)

returns an instance from a serialised dictionary

core.alphabet.CharAlphabet.get_kmer_alphabet(k, include_gap=True)

returns kmer alphabet with words of size k

Name	Type	Description	Default
k	int	word size	required
include_gap	bool	if True, and self.gap_char, we set KmerAlphabet.gap_char = self.gap_char * k	`True`

If self.missing_char is present, it is included in the new alphabet as missing_char * k

core.alphabet.CharAlphabet.get_subset(motif_subset, excluded=False)

Returns a new Alphabet object containing a subset of motifs in self.

Raises an exception if any of the items in the subset are not already in self.

core.alphabet.CharAlphabet.is_valid(seq)

seq is valid for alphabet

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

returns a sequence of indices for the characters in seq

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

core.alphabet.CharAlphabet.to_json()

returns a serialisable string

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

returns a serialisable dictionary

core.alphabet.CharAlphabet.with_gap_motif(
    gap_char='-',
    missing_char='?',
    include_missing=False,
    gap_as_state=False,
)

returns new monomer alphabet with gap and missing characters added

Name	Type	Description	Default
gap_char	str \| bytes	the IUPAC gap character “-”	`'-'`
missing_char	str \| bytes \| None	the IUPAC missing character “?”	`'?'`
include_missing	bool	if True, and self.missing_char, it is included in the new alphabet	`False`
gap_as_state	bool	include the gap character as a state in the alphabet, drops gap_char attribute in resulting KmerAlphabet	`False`