def count_vectors(table: biom.Table,
phylogeny: skbio.TreeNode,
method: str = 'weighted_unifrac') -> biom.Table:
table = _map_observations(table)
pruned_phylo = prune_features_from_phylogeny(table, phylogeny)
pruned_phylo = rename_nodes(pruned_phylo)
table = table.sort(axis='observation')
otu_ids = np.asarray(table.ids('observation'))
counts = np.asarray(table.matrix_data.todense().transpose())
features, tree_index = _run_unifrac(counts, otu_ids, pruned_phylo, method)
return biom.Table(data=features.transpose(),
observation_ids=rename_otus(tree_index),
sample_ids=table.ids())
