Alphabet

class pyopal.Alphabet

A class for ordinal encoding of sequences.

Added in version 0.5.0.

__getitem__(key, /)

Return self[key].

__init__(*args, **kwargs)

__len__()

Return len(self).

__str__()

Return str(self).

decode(encoded)

Decode an ordinal-encoded sequence using the alphabet.

Parameters:

sequence (byte-like object) – The sequence to decode.

Raises:

ValueError – When the sequence contains invalid indices.

Example

>>> alphabet = Alphabet("ACGT")
>>> alphabet.decode(bytearray([2, 0, 3, 0, 1, 0]))
'GATACA'

decode_into(encoded, sequence)

Decode a sequence from ordinal-encoding into the given buffer.

encode(sequence)

Encode a sequence to an ordinal-encoded sequence using the alphabet.

Parameters:

sequence (str or byte-like object) – The sequence to encode.

Raises:

• ValueError – When the sequence contains invalid characters, or

• unknown sequence characters while the alphabet contains no –

• wildcard character. –

Example

>>> alphabet = Alphabet("ACGT")
>>> alphabet.encode("GATACA")
b'\x02\x00\x03\x00\x01\x00'

encode_into(sequence, encoded)

Encode a sequence to ordinal-encoding into the given buffer.