pbtools¶
Perform analysis on protein sequences encoded as Protein Blocks
Provide functions to compute a Mutual Information matrix from sequences.
-
pbtools.interaction_graph(matrix)¶ Create a networkx graph object from a (square) matrix.
- Parameters
matrix (numpy.ndarray) –
Matrix of mutual information, the information for the edges is taken from the upper matrix- Returns
graph – The graph with MI as weighted edges and positions as nodes
- Return type
networkx.Graph()
- Raises
AssertionError – If the matrix is not square
-
pbtools.mutual_information(pos1, pos2)¶ Computes the Mutual Information from 2 Series of Protein Blocks.
- Parameters
pos1 (pandas.Series) – Protein Blocks of a given sequence position.
pos2 (pandas.Series) – Protein Blocks of a given sequence position.
- Returns
MI – Mutual Information of the 2 positions.
- Return type
float
- Raises
AssertionError – If Series are not provided or have different lengths.
-
pbtools.mutual_information_matrix(sequences)¶ Return the matrix of Mutual Information for all positions.
- Parameters
sequences (list of str) – Sequences obtained from the file(s)
- Returns
MI_matrix – Matrix of Mutual Informations.
- Return type
numpy.ndarray