Generate distance matrix among samples by unifrac distance

dist_unifrac.py

import numpy as np
from skbio import TreeNode
from skbio.diversity import beta_diversity

tree = TreeNode.read("gg_13_8_otus/trees/61_otus_unannotated.tree")
sample_ids = [f"sample{i}" for i in range(6)]
with open("gg_13_8_otus/taxonomy/61_otu_taxonomy.txt", "r") as f:
    otu_ids = [each.strip().split("\t")[0] for each in f.readlines()]
data = np.random.randint(0, 100, size=(len(sample_ids), len(otu_ids))).tolist()

unifrac = beta_diversity("weighted_unifrac", data, ids=sample_ids, tree=tree, otu_ids=otu_ids)
unifrac.to_data_frame()