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
