CharAlphabet

class CharAlphabet(chars: Sequence[StrORBytes] | str | bytes, gap: str | None = None, missing: str | None = None)

representing fundamental monomer character sets.

Attributes:

gap_char

gap_index

missing_char

missing_index

moltype

motif_len

num_canonical

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(-> str  -> str)	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_motif_len()	the size of each member of the alphabet
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(-> bool  -> bool)	seq is valid for alphabet
to_indices(-> ~numpy.ndarray[tuple[int, ...)	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

get_word_alphabet

Notes

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

array_to_bytes(seq: ndarray[tuple[int, ...], dtype[integer]]) → bytes

returns seq as a byte string

as_bytes() → bytes

returns self as a byte string

convert_seq_array_to(*, alphabet: Self, seq: ndarray[tuple[int, ...], dtype[integer]], check_valid: bool = True) → ndarray[tuple[int, ...], dtype[integer]]

converts a numpy array with indices from self to other

Parameters:

alphabet

alphabet to convert to

seq

ndarray of uint8 integers

check_valid

validates both input and out sequences are valid for self and other respectively. Validation failure raises an AlphabetError.

Returns:

the indices of characters in common between self and other

are swapped

count(value, /)

Return number of occurrences of value.

from_indices(seq: StrORBytesORArray) → str

from_indices(seq: str) → str

from_indices(seq: bytes) → str

from_indices(seq: ndarray) → str

returns a string from a sequence of indices

classmethod from_rich_dict(data: dict) → Self

returns an instance from a serialised dictionary

property gap_char: str | None

property gap_index: int | None

get_kmer_alphabet(k: int, include_gap: bool = True) → KmerAlphabet

returns kmer alphabet with words of size k

Parameters:

k

word size

include_gap

if True, and self.gap_char, we set KmerAlphabet.gap_char = self.gap_char * k

Notes

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

get_motif_len() → int

the size of each member of the alphabet

get_subset(motif_subset: Sequence[str] | Sequence[bytes], excluded: bool = False) → Self

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.

get_word_alphabet(k: int, include_gap: bool = True) → KmerAlphabet

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

Return first index of value.

Raises ValueError if the value is not present.

is_valid(seq: StrORBytesORArray) → bool

is_valid(seq: str) → bool

is_valid(seq: bytes) → bool

is_valid(seq: ndarray) → bool

seq is valid for alphabet

property missing_char: str | None

property missing_index: int | None

property moltype: MolType | None

property motif_len: int

property num_canonical: int

to_indices(seq: StrORBytesORArray | tuple) → ndarray[tuple[int, ...], dtype[integer]]

to_indices(seq: tuple) → ndarray[tuple[int, ...], dtype[integer]]

to_indices(seq: bytes) → ndarray[tuple[int, ...], dtype[integer]]

to_indices(seq: str) → ndarray[tuple[int, ...], dtype[integer]]

to_indices(seq: ndarray) → ndarray[tuple[int, ...], dtype[integer]]

returns a sequence of indices for the characters in seq

to_json() → str

returns a serialisable string

to_rich_dict(for_pickle: bool = False) → dict[str, Any]

returns a serialisable dictionary

with_gap_motif(gap_char: str = '-', missing_char: str = '?', include_missing: bool = False, gap_as_state: bool = False) → Self

returns new monomer alphabet with gap and missing characters added

Parameters:

gap_char

the IUPAC gap character “-”

missing_char

the IUPAC missing character “?”

include_missing

if True, and self.missing_char, it is included in the new alphabet

gap_as_state

include the gap character as a state in the alphabet, drops gap_char attribute in resulting KmerAlphabet