matrix.py 文件源码

def read_triangular(filepath):
    """Open Pi matrix output from SLICE.

    All matrix opening functions return first the
    genomic windows corresponding to the axes of the
    proximity matrix, then the proximity matrix itself.
    Since SLICE output matrices do not embed the genomic
    locations of the windows, the first return value is
    None.

    :param str filepath: Path to the SLICE output file
    :returns: (None, SLICE Pi matrix)
    """

    with open(filepath) as in_data:
        arr = [[float(i) for i in line.split()] for line in in_data]
    size = len(arr[-1])
    proximity_matrix = np.zeros((size, size))
    lower_i = np.tril_indices_from(proximity_matrix)
    upper_i = np.triu_indices_from(proximity_matrix)
    proximity_matrix[:] = np.NAN
    proximity_matrix[lower_i] = list(itertools.chain(*arr))
    proximity_matrix[upper_i] = proximity_matrix.T[upper_i]
    proximity_matrix[proximity_matrix > 1.] = np.NAN

    return None, proximity_matrix