def parse_a3m()

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

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

def parse_a3m(a3m_string: str) -> Msa:
  """Parses sequences and deletion matrix from a3m format alignment.

  Args:
    a3m_string: The string contents of a a3m file. The first sequence in the
      file should be the query sequence.

  Returns:
    A tuple of:
      * A list of sequences that have been aligned to the query. These
        might contain duplicates.
      * The deletion matrix for the alignment as a list of lists. The element
        at `deletion_matrix[i][j]` is the number of residues deleted from
        the aligned sequence i at residue position j.
      * A list of descriptions, one per sequence, from the a3m file.
  """
  sequences, descriptions = parse_fasta(a3m_string)
  deletion_matrix = []
  for msa_sequence in sequences:
    deletion_vec = []
    deletion_count = 0
    for j in msa_sequence:
      if j.islower():
        deletion_count += 1
      else:
        deletion_vec.append(deletion_count)
        deletion_count = 0
    deletion_matrix.append(deletion_vec)

  # Make the MSA matrix out of aligned (deletion-free) sequences.
  deletion_table = str.maketrans('', '', string.ascii_lowercase)
  aligned_sequences = [s.translate(deletion_table) for s in sequences]
  return Msa(sequences=aligned_sequences,
             deletion_matrix=deletion_matrix,
             descriptions=descriptions)