biotite.sequence.LetterAlphabet¶

class biotite.sequence.LetterAlphabet(symbols)[source]¶

Bases: Alphabet

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, as_bytes=False)¶

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_multiple(code, as_bytes=False)¶

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: 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.

encode(symbol)¶

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, dtype=None)¶

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