def test_unweighted_root_eval_issue_46(self):
tree = self.get_data_path('crawford.tre')
table = self.get_data_path('crawford.biom')
table_inmem = load_table(table)
tree_inmem = skbio.TreeNode.read(tree)
ids = table_inmem.ids()
otu_ids = table_inmem.ids(axis='observation')
cnts = table_inmem.matrix_data.astype(int).toarray().T
exp = skbio.diversity.beta_diversity('unweighted_unifrac',
cnts,
ids=ids,
otu_ids=otu_ids,
tree=tree_inmem)
obs = ssu(table, tree, 'unweighted', False, 1.0, False, 1)
npt.assert_almost_equal(obs.data, exp.data)
obs2 = unweighted(table, tree)
npt.assert_almost_equal(obs2.data, exp.data)
tmpfile = '/tmp/uf_ta_1.md5'
unweighted_to_file(table, tree, tmpfile, pcoa_dims=0)
try:
obs3 = h5unifrac(tmpfile)
npt.assert_almost_equal(obs3.data, exp.data)
finally:
os.unlink(tmpfile)
def unweighted_unifrac(table: BIOMV210Format,
phylogeny: NewickFormat,
threads: int = 1,
bypass_tips: bool = False) -> skbio.DistanceMatrix:
return unifrac.unweighted(str(table),
str(phylogeny),
threads=threads,
variance_adjusted=False,
bypass_tips=bypass_tips)
def test_unweighted_fp32_inmem(self):
tree_fp = self.get_data_path('crawford.tre')
table_fp = self.get_data_path('crawford.biom')
table = load_table(table_fp)
tree = skbio.TreeNode.read(tree_fp)
ids = table.ids()
otu_ids = table.ids(axis='observation')
cnts = table.matrix_data.astype(int).toarray().T
exp = skbio.diversity.beta_diversity('unweighted_unifrac',
cnts,
ids=ids,
otu_ids=otu_ids,
tree=tree)
obs = ssu_inmem(table, tree, 'unweighted_fp32', False, 1.0, False, 1)
npt.assert_almost_equal(obs.data, exp.data, decimal=6)
obs2 = unweighted(table_fp, tree_fp)
npt.assert_almost_equal(obs2.data, exp.data)