def _get_indices()

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

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

def _get_indices(sequence: str, start: int) -> List[int]:
  """Returns indices for non-gap/insert residues starting at the given index."""
  indices = []
  counter = start
  for symbol in sequence:
    # Skip gaps but add a placeholder so that the alignment is preserved.
    if symbol == '-':
      indices.append(-1)
    # Skip deleted residues, but increase the counter.
    elif symbol.islower():
      counter += 1
    # Normal aligned residue. Increase the counter and append to indices.
    else:
      indices.append(counter)
      counter += 1
  return indices