`LetterAlphabet`#

class biotite.sequence.LetterAlphabet(symbols: Iterable[str | bytes] | str | bytes)[source]#

Bases: Alphabet[str]

LetterAlphabet is a an Alphabet subclass specialized for letter based alphabets, like DNA or protein sequence alphabets. The alphabet size is limited to the 94 printable, non-whitespace characters. Internally the symbols are saved as bytes objects. The encoding and decoding process is a lot faster than for a normal Alphabet.

The performance gain comes through the use of NumPy and Cython for encoding and decoding, without the need of a dictionary.

Parameters:

symbolsiterable object or str or bytes: The symbols, that are allowed in this alphabet. The corresponding code for a symbol, is the index of that symbol in this list.

decode(code: int, as_bytes: bool = False) → str#

Use the alphabet to decode a symbol code.

Parameters:

codeint: The symbol code to be decoded.

Returns:

symbolobject: The symbol corresponding to code.

Raises:

AlphabetError: If code is not a valid code in the alphabet.

decode_into_byte(code: int) → bytes#

Decode a code into a single-byte symbol.

Parameters:

codeint: The code to decode.

Returns:

symbolbytes: The decoded symbol as a single-byte object.

decode_multiple(code: ndarray[tuple[K], dtype[integer]] | Iterable[int], as_bytes: bool = False) → ndarray[tuple[K], dtype[character]]#

Decode a sequence code into a list of symbols.

Parameters:

codendarray, dtype=uint8: The sequence code to decode. Works fastest if a ndarray is provided.
as_bytesbool, optional: DEPRECATED: Use decode_multiple_into_bytes() instead. If true, the output array will contain bytes (dtype ‘S1’). Otherwise, the the output array will contain str (dtype ‘U1’).

Returns:

symbolsndarray, dtype=’U1’ or dtype=’S1’: The decoded list of symbols.

decode_multiple_into_bytes(code: ndarray[tuple[K], dtype[integer]] | Iterable[int]) → ndarray[tuple[K], dtype[bytes_]]#

Decode a sequence code into a single-byte symbol array.

This is a faster alternative to decode_multiple() when single-byte symbols are desired, as it avoids the conversion to Unicode characters.

Parameters:

codendarray, dtype=uint8: The sequence code to decode. Works fastest if a ndarray is provided.

Returns:

symbolsndarray, dtype=’S1’: The decoded list of symbols.

encode(symbol: str | bytes) → int#

Use the alphabet to encode a symbol.

Parameters:

symbolobject: The object to encode into a symbol code.

Returns:

codeint: The symbol code of symbol.

Raises:

AlphabetError: If symbol is not in the alphabet.

Encode multiple symbols.

Parameters:

symbolsiterable object or str or bytes: The symbols to encode. The method is fastest when a ndarray, str or bytes object containing the symbols is provided, instead of e.g. a list.
dtypedtype, optional: For compatibility with superclass. The value is ignored.

Returns: