deepfold.data.search.parsers.parse_stockholm

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

Parses sequences and deletion matrix from stockholm format alignment.

Parameters:

• stockholm_string – The string contents of a stockholm file.

• sequence. (The first sequence in the file should be the query)

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.

• The names of the targets matched,

  including the jackhmmer subsequence suffix.

Return type:

A tuple of