_method.py 文件源码

def beta_phylogenetic(table: biom.Table, phylogeny: skbio.TreeNode,
                      metric: str, n_jobs: int=1)-> skbio.DistanceMatrix:
    if metric not in phylogenetic_metrics():
        raise ValueError("Unknown phylogenetic metric: %s" % metric)
    if table.is_empty():
        raise ValueError("The provided table object is empty")
    if n_jobs != 1 and metric == 'weighted_unifrac':
        raise ValueError("Weighted UniFrac is not parallelizable")

    counts = table.matrix_data.toarray().astype(int).T
    sample_ids = table.ids(axis='sample')
    feature_ids = table.ids(axis='observation')

    try:
        results = skbio.diversity.beta_diversity(
            metric=metric,
            counts=counts,
            ids=sample_ids,
            otu_ids=feature_ids,
            tree=phylogeny,
            pairwise_func=sklearn.metrics.pairwise_distances,
            n_jobs=n_jobs
        )
    except skbio.tree.MissingNodeError as e:
        message = str(e).replace('otu_ids', 'feature_ids')
        message = message.replace('tree', 'phylogeny')
        raise skbio.tree.MissingNodeError(message)

    return results