deepfold.data.search.parsers.parse_a3m

deepfold.data.search.parsers.parse_a3m(a3m_string: str) → Tuple[Sequence[str], Sequence[Sequence[int]], Sequence[str]]

Parses sequences and deletion matrix from a3m format alignment.

Parameters:

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

Returns:

• 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.

Return type:

A tuple of