CharAlphabet

class CharAlphabet(chars: Sequence[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
count(value, /)	Return number of occurrences of value.
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
index(value[, start, stop])	Return first index of value.
to_json()	returns a serialisable string
to_rich_dict()	returns a serialisable dictionary
with_gap_motif([gap_char, missing_char])	returns new monomer alphabet with gap and missing characters added

from_indices
get_motif_len
get_word_alphabet
is_valid
to_indices

Notes

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

array_to_bytes(seq: ndarray) → bytes

returns seq as a byte string

as_bytes() → bytes

returns self as a byte string

count(value, /)

Return number of occurrences of value.

from_indices(seq: str | bytes | ndarray) → str

from_indices(seq: str) → str

from_indices(seq: bytes) → str

from_indices(seq: ndarray) → str

classmethod from_rich_dict(data: dict) → CharAlphabet

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

get_motif_len() → int

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: str | bytes | ndarray) → bool

is_valid(seq: str) → bool

is_valid(seq: bytes) → bool

is_valid(seq: ndarray) → bool

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: str | bytes | ndarray) → ndarray[int]

to_indices(seq: bytes) → ndarray[int]

to_indices(seq: str) → ndarray[int]

to_indices(seq: ndarray) → ndarray[int]

to_json() → str

returns a serialisable string

to_rich_dict() → dict

returns a serialisable dictionary

with_gap_motif(gap_char='-', missing_char='?')

returns new monomer alphabet with gap and missing characters added

Parameters:

gap_char

the IUPAC gap character “-”

missing_char

the IUPAC missing character “?”