def sequence_to_onehot()

in src/analysis/residue_constants.py [0:0]

• 19 lines of code
• 6 McCabe index (conditional complexity)

def sequence_to_onehot(
    sequence: str,
    mapping: Mapping[str, int],
    map_unknown_to_x: bool = False) -> np.ndarray:
  """Maps the given sequence into a one-hot encoded matrix.

  Args:
    sequence: An amino acid sequence.
    mapping: A dictionary mapping amino acids to integers.
    map_unknown_to_x: If True, any amino acid that is not in the mapping will be
      mapped to the unknown amino acid 'X'. If the mapping doesn't contain
      amino acid 'X', an error will be thrown. If False, any amino acid not in
      the mapping will throw an error.

  Returns:
    A numpy array of shape (seq_len, num_unique_aas) with one-hot encoding of
    the sequence.

  Raises:
    ValueError: If the mapping doesn't contain values from 0 to
      num_unique_aas - 1 without any gaps.
  """
  num_entries = max(mapping.values()) + 1

  if sorted(set(mapping.values())) != list(range(num_entries)):
    raise ValueError('The mapping must have values from 0 to num_unique_aas-1 '
                     'without any gaps. Got: %s' % sorted(mapping.values()))

  one_hot_arr = np.zeros((len(sequence), num_entries), dtype=np.int32)

  for aa_index, aa_type in enumerate(sequence):
    if map_unknown_to_x:
      if aa_type.isalpha() and aa_type.isupper():
        aa_id = mapping.get(aa_type, mapping['X'])
      else:
        raise ValueError(f'Invalid character in the sequence: {aa_type}')
    else:
      aa_id = mapping[aa_type]
    one_hot_arr[aa_index, aa_id] = 1

  return one_hot_arr