def test(): data, otus, samples = ctwc__data_handler.get_sample_biom_table() tree = ctwc__data_handler.get_gg_97_otu_tree() _, cols_dist = ctwc__distance_matrix.get_distance_matrices(data, tree, samples, otus, skip_rows=True) picked_indices, max_rank, filtered_data, filtered_dist_matrix, _ , _ = filter_cols_by_top_rank(data, cols_dist, otus, True) INFO("Picked {0} indices".format(len(picked_indices))) clust, labels, ag = ctwc__cluster_1d.cluster_rows(filtered_data.transpose(), cols_dist)
def get_data(use_real_data): if use_real_data: INFO("Using real data") data, otus, samples, table = ctwc__data_handler.get_sample_biom_table() tree = ctwc__data_handler.get_gg_97_otu_tree() else: INFO("Using synthetic data") samples = ctwc__data_handler.get_default_samples() otus = ctwc__data_handler.get_default_otus() tree = ctwc__data_handler.get_default_tree(otus) data = ctwc__data_handler.get_default_data(otus, samples) table = None return samples, otus, tree, data, table