def clean_and_validate_sequence()

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

• 21 lines of code
• 5 McCabe index (conditional complexity)

def clean_and_validate_sequence(
    input_sequence: str, min_length: int, max_length: int) -> str:
  """Checks that the input sequence is ok and returns a clean version of it."""
  # Remove all whitespaces, tabs and end lines; upper-case.
  clean_sequence = input_sequence.translate(
      str.maketrans('', '', ' \n\t')).upper()
  aatypes = set(residue_constants.restypes)  # 20 standard aatypes.
  if not set(clean_sequence).issubset(aatypes):
    raise ValueError(
        f'Input sequence contains non-amino acid letters: '
        f'{set(clean_sequence) - aatypes}. AlphaFold only supports 20 standard '
        'amino acids as inputs.')
  if len(clean_sequence) < min_length:
    raise ValueError(
        f'Input sequence is too short: {len(clean_sequence)} amino acids, '
        f'while the minimum is {min_length}')
  if len(clean_sequence) > max_length:
    raise ValueError(
        f'Input sequence is too long: {len(clean_sequence)} amino acids, while '
        f'the maximum is {max_length}. You may be able to run it with the full '
        f'AlphaFold system depending on your resources (system memory, '
        f'GPU memory).')
  return clean_sequence