def read_cluster_file(cluster_file_dir):
    """Read the clustered pockets as a list of lists."""
    f = open(cluster_file_dir, 'r')
    data_text = f.read()
    f.close()
    data_text = data_text.split('\n')

    while('' in data_text):
        data_text.remove('')

    clusters = []
    for x in data_text:
        cluster = x.split()[3:]
        cluster = [x.split(',')[0] for x in cluster]
        clusters.append(cluster)

    return clusters