_method.py 文件源码

def beta_phylogenetic_alt(table: BIOMV210Format, phylogeny: NewickFormat,
                          metric: str, n_jobs: int=1,
                          variance_adjusted: bool=False,
                          alpha: float=None,
                          bypass_tips: bool=False) -> skbio.DistanceMatrix:

    metrics = phylogenetic_metrics_alt_dict()
    generalized_unifrac = 'generalized_unifrac'

    if metric not in metrics:
        raise ValueError("Unknown metric: %s" % metric)

    if alpha is not None and metric != generalized_unifrac:
        raise ValueError('The alpha parameter is only allowed when the choice'
                         ' of metric is generalized_unifrac')

    # this behaviour is undefined, so let's avoid a seg fault
    cpus = psutil.cpu_count(logical=False)
    if n_jobs > cpus:
        raise ValueError('The value of n_jobs cannot exceed the number of '
                         'processors (%d) available in this system.' % cpus)

    if metric == generalized_unifrac:
        alpha = 1.0 if alpha is None else alpha
        f = partial(metrics[metric], alpha=alpha)
    else:
        f = metrics[metric]

    # unifrac processes tables and trees should be filenames
    return f(str(table), str(phylogeny), threads=n_jobs,
             variance_adjusted=variance_adjusted, bypass_tips=bypass_tips)