def test_faith_pd_none_observed(self):
actual = faith_pd(np.array([], dtype=int), np.array([], dtype=int), self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
actual = faith_pd([0, 0, 0, 0, 0], self.oids1, self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
def test_faith_pd_all_observed(self):
actual = faith_pd([1, 1, 1, 1, 1], self.oids1, self.t1)
expected = sum(n.length for n in self.t1.traverse() if n.length is not None)
self.assertAlmostEqual(actual, expected)
actual = faith_pd([1, 2, 3, 4, 5], self.oids1, self.t1)
expected = sum(n.length for n in self.t1.traverse() if n.length is not None)
self.assertAlmostEqual(actual, expected)
def test_faith_pd_none_observed(self):
actual = faith_pd(np.array([], dtype=int), np.array([], dtype=int),
self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
actual = faith_pd([0, 0, 0, 0, 0], self.oids1, self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
def test_faith_pd_all_observed(self):
actual = faith_pd([1, 1, 1, 1, 1], self.oids1, self.t1)
expected = sum(n.length for n in self.t1.traverse()
if n.length is not None)
self.assertAlmostEqual(actual, expected)
actual = faith_pd([1, 2, 3, 4, 5], self.oids1, self.t1)
expected = sum(n.length for n in self.t1.traverse()
if n.length is not None)
self.assertAlmostEqual(actual, expected)
def test_faith_pd_minimal_trees(self):
# expected values computed by hand
# zero tips
tree = TreeNode.read(StringIO(u'root;'))
actual = faith_pd(np.array([], dtype=int), [], tree)
expected = 0.0
self.assertEqual(actual, expected)
# two tips
tree = TreeNode.read(StringIO(u'(OTU1:0.25, OTU2:0.25)root;'))
actual = faith_pd([1, 0], ['OTU1', 'OTU2'], tree)
expected = 0.25
self.assertEqual(actual, expected)
def test_faith_pd_minimal_trees(self):
# expected values computed by hand
# zero tips
tree = TreeNode.read(StringIO(u'root;'))
actual = faith_pd(np.array([], dtype=int), [], tree)
expected = 0.0
self.assertEqual(actual, expected)
# two tips
tree = TreeNode.read(StringIO(u'(OTU1:0.25, OTU2:0.25)root;'))
actual = faith_pd([1, 0], ['OTU1', 'OTU2'], tree)
expected = 0.25
self.assertEqual(actual, expected)
def test_faith_pd_root_not_observed(self):
# expected values computed by hand
tree = TreeNode.read(StringIO(u"((OTU1:0.1, OTU2:0.2):0.3, (OTU3:0.5, OTU4:0.7):1.1)" u"root;"))
otu_ids = ["OTU%d" % i for i in range(1, 5)]
# root node not observed, but branch between (OTU1, OTU2) and root
# is considered observed
actual = faith_pd([1, 1, 0, 0], otu_ids, tree)
expected = 0.6
self.assertAlmostEqual(actual, expected)
# root node not observed, but branch between (OTU3, OTU4) and root
# is considered observed
actual = faith_pd([0, 0, 1, 1], otu_ids, tree)
expected = 2.3
self.assertAlmostEqual(actual, expected)
def test_faith_pd(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# phylogenetic diversity implementation
actual = faith_pd(self.b1[0], self.oids1, self.t1)
expected = 4.5
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[1], self.oids1, self.t1)
expected = 4.75
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[2], self.oids1, self.t1)
expected = 4.75
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[3], self.oids1, self.t1)
expected = 4.75
self.assertAlmostEqual(actual, expected)
def test_faith_pd(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# phylogenetic diversity implementation
actual = faith_pd(self.b1[0], self.oids1, self.t1)
expected = 4.5
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[1], self.oids1, self.t1)
expected = 4.75
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[2], self.oids1, self.t1)
expected = 4.75
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[3], self.oids1, self.t1)
expected = 4.75
self.assertAlmostEqual(actual, expected)
def test_faith_pd_root_not_observed(self):
# expected values computed by hand
tree = TreeNode.read(
StringIO(u'((OTU1:0.1, OTU2:0.2):0.3, (OTU3:0.5, OTU4:0.7):1.1)'
u'root;'))
otu_ids = ['OTU%d' % i for i in range(1, 5)]
# root node not observed, but branch between (OTU1, OTU2) and root
# is considered observed
actual = faith_pd([1, 1, 0, 0], otu_ids, tree)
expected = 0.6
self.assertAlmostEqual(actual, expected)
# root node not observed, but branch between (OTU3, OTU4) and root
# is considered observed
actual = faith_pd([0, 0, 1, 1], otu_ids, tree)
expected = 2.3
self.assertAlmostEqual(actual, expected)
def test_faith_pd(self):
# calling faith_pd through alpha_diversity gives same results as
# calling it directly
expected = []
for e in self.table1:
expected.append(faith_pd(e, tree=self.tree1, otu_ids=self.oids1))
expected = pd.Series(expected)
actual = alpha_diversity('faith_pd', self.table1, tree=self.tree1,
otu_ids=self.oids1)
assert_series_almost_equal(actual, expected)
# alt input table and tree
expected = []
for e in self.table2:
expected.append(faith_pd(e, tree=self.tree2, otu_ids=self.oids2))
expected = pd.Series(expected)
actual = alpha_diversity('faith_pd', self.table2, tree=self.tree2,
otu_ids=self.oids2)
assert_series_almost_equal(actual, expected)
def test_faith_pd(self):
# calling faith_pd through alpha_diversity gives same results as
# calling it directly
expected = []
for e in self.table1:
expected.append(faith_pd(e, tree=self.tree1, otu_ids=self.oids1))
expected = pd.Series(expected)
actual = alpha_diversity('faith_pd', self.table1, tree=self.tree1,
otu_ids=self.oids1)
assert_series_almost_equal(actual, expected)
# alt input table and tree
expected = []
for e in self.table2:
expected.append(faith_pd(e, tree=self.tree2, otu_ids=self.oids2))
expected = pd.Series(expected)
actual = alpha_diversity('faith_pd', self.table2, tree=self.tree2,
otu_ids=self.oids2)
assert_series_almost_equal(actual, expected)
def test_faith_pd_extra_tips(self):
# results are the same despite presences of unobserved tips in tree
actual = faith_pd(self.b1[0], self.oids1, self.t1_w_extra_tips)
expected = faith_pd(self.b1[0], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[1], self.oids1, self.t1_w_extra_tips)
expected = faith_pd(self.b1[1], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[2], self.oids1, self.t1_w_extra_tips)
expected = faith_pd(self.b1[2], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[3], self.oids1, self.t1_w_extra_tips)
expected = faith_pd(self.b1[3], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
def test_faith_pd_extra_tips(self):
# results are the same despite presences of unobserved tips in tree
actual = faith_pd(self.b1[0], self.oids1, self.t1_w_extra_tips)
expected = faith_pd(self.b1[0], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[1], self.oids1, self.t1_w_extra_tips)
expected = faith_pd(self.b1[1], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[2], self.oids1, self.t1_w_extra_tips)
expected = faith_pd(self.b1[2], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
actual = faith_pd(self.b1[3], self.oids1, self.t1_w_extra_tips)
expected = faith_pd(self.b1[3], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
def count_alpha_diversity(series: pd.Series, rooted_tree: TreeNode = None):
d = {
k: ALPHA_DIVERSITY_FUNCTIONS[k](series.values)
for k in ALPHA_DIVERSITY_FUNCTIONS
}
d["Inverse Simpson Index"] = 1.0 / d["Simpson Index"]
d["Gini–Simpson Index"] = 1.0 - d["Simpson Index"]
if rooted_tree is not None:
d["Faith Diversity"] = a.faith_pd(series.values, series.index.values,
rooted_tree)
out = dict2pd_series(d)
out.name = series.name
return out
def test_faith_pd_qiime_tiny_test(self):
# the following table and tree are derived from the QIIME 1.9.1
# "tiny-test" data
tt_table_fp = get_data_path(os.path.join("qiime-191-tt", "otu-table.tsv"), "data")
tt_tree_fp = get_data_path(os.path.join("qiime-191-tt", "tree.nwk"), "data")
self.q_table = pd.read_csv(tt_table_fp, sep="\t", skiprows=1, index_col=0)
self.q_tree = TreeNode.read(tt_tree_fp)
expected_fp = get_data_path(os.path.join("qiime-191-tt", "faith-pd.txt"), "data")
expected = pd.read_csv(expected_fp, sep="\t", index_col=0)
for sid in self.q_table.columns:
actual = faith_pd(self.q_table[sid], otu_ids=self.q_table.index, tree=self.q_tree)
self.assertAlmostEqual(actual, expected["PD_whole_tree"][sid])
def test_faith_pd_qiime_tiny_test(self):
# the following table and tree are derived from the QIIME 1.9.1
# "tiny-test" data
tt_table_fp = get_data_path(
os.path.join('qiime-191-tt', 'otu-table.tsv'), 'data')
tt_tree_fp = get_data_path(os.path.join('qiime-191-tt', 'tree.nwk'),
'data')
self.q_table = pd.read_csv(tt_table_fp,
sep='\t',
skiprows=1,
index_col=0)
self.q_tree = TreeNode.read(tt_tree_fp)
expected_fp = get_data_path(
os.path.join('qiime-191-tt', 'faith-pd.txt'), 'data')
expected = pd.read_csv(expected_fp, sep='\t', index_col=0)
for sid in self.q_table.columns:
actual = faith_pd(self.q_table[sid],
otu_ids=self.q_table.index,
tree=self.q_tree)
self.assertAlmostEqual(actual, expected['PD_whole_tree'][sid])
def test_faith_pd_minimal(self):
# two tips
tree = TreeNode.read(StringIO('(OTU1:0.25, OTU2:0.25)root;'))
actual = faith_pd([1, 0], ['OTU1', 'OTU2'], tree)
expected = 0.25
self.assertEqual(actual, expected)
def test_faith_pd_minimal(self):
# two tips
tree = TreeNode.read(StringIO(u'(OTU1:0.25, OTU2:0.25)root;'))
actual = faith_pd([1, 0], ['OTU1', 'OTU2'], tree)
expected = 0.25
self.assertEqual(actual, expected)
