def test_unweighted_unifrac_symmetry(self):
for i in range(len(self.table1)):
for j in range(len(self.table1)):
actual = unweighted_unifrac(
self.table1[i], self.table1[j], self.oids1, self.t1)
expected = unweighted_unifrac(
self.table1[j], self.table1[i], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
def test_unweighted_unifrac_symmetry(self):
for i in range(len(self.b1)):
for j in range(len(self.b1)):
actual = unweighted_unifrac(self.b1[i], self.b1[j], self.oids1,
self.t1)
expected = unweighted_unifrac(self.b1[j], self.b1[i],
self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
def test_unweighted_extra_tips(self):
# UniFrac values are the same despite unobserved tips in the tree
for i in range(len(self.b1)):
for j in range(len(self.b1)):
actual = unweighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1_w_extra_tips)
expected = unweighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
def test_unweighted_extra_tips(self):
# UniFrac values are the same despite unobserved tips in the tree
for i in range(len(self.b1)):
for j in range(len(self.b1)):
actual = unweighted_unifrac(self.b1[i], self.b1[j], self.oids1,
self.t1_w_extra_tips)
expected = unweighted_unifrac(self.b1[i], self.b1[j],
self.oids1, self.t1)
self.assertAlmostEqual(actual, expected)
def test_unweighted_unifrac_non_overlapping(self):
# these communities only share the root node
actual = unweighted_unifrac(
self.table1[4], self.table1[5], self.oids1, self.t1)
expected = 1.0
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
[1, 1, 1, 0, 0], [0, 0, 0, 1, 1], self.oids1, self.t1)
expected = 1.0
self.assertAlmostEqual(actual, expected)
def test_unweighted_unifrac_non_overlapping(self):
# these communities only share the root node
actual = unweighted_unifrac(self.b1[4], self.b1[5], self.oids1,
self.t1)
expected = 1.0
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac([1, 1, 1, 0, 0], [0, 0, 0, 1, 1],
self.oids1, self.t1)
expected = 1.0
self.assertAlmostEqual(actual, expected)
def test_unweighted_unifrac_zero_counts(self):
actual = unweighted_unifrac([1, 1, 1, 0, 0], [0, 0, 0, 0, 0],
self.oids1, self.t1)
expected = 1.0
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac([0, 0, 0, 0, 0], [0, 0, 0, 0, 0],
self.oids1, self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac([], [], [], self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
def test_unweighted_minimal_trees(self):
# expected values computed by hand
# zero tips
tree = TreeNode.read(StringIO(u'root;'))
actual = unweighted_unifrac([], [], [], tree)
expected = 0.0
self.assertEqual(actual, expected)
# two tips
tree = TreeNode.read(StringIO(u'(OTU1:0.25, OTU2:0.25)root;'))
actual = unweighted_unifrac([1, 0], [0, 0], ['OTU1', 'OTU2'], tree)
expected = 1.0
self.assertEqual(actual, expected)
def test_unweighted_unifrac_zero_counts(self):
actual = unweighted_unifrac(
[1, 1, 1, 0, 0], [0, 0, 0, 0, 0], self.oids1, self.t1)
expected = 1.0
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], self.oids1, self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
[], [], [], self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
def compute_beta_unifraq(df, m):
from skbio.diversity.beta import unweighted_unifrac, weighted_unifrac
# get the phylogenetic tree and drop OTUs that are not NCBI annotated
otu_ids = list(df.index.values)
tree, notfound = load_taxonomy_tree(otu_ids)
df = df.drop(list(notfound))
# The numpy matrix of counts, in which the rows are sample counts
mt = df.values.T.astype(np.dtype('int64'))
# Sample list
sl = list(df.columns.values)
# OTU list
otu_ids = list(df.index.values)
# The beta diversity matrix
nsamples = len(sl)
bm = np.zeros((nsamples, nsamples))
# Compute the pairwise unifraq
for i in range(nsamples):
for j in range(i):
u_counts = mt[i]
v_counts = mt[j]
if m == "unifraq":
uu = unweighted_unifrac(u_counts, v_counts, otu_ids, tree)
if m == "wunifraq":
uu = weighted_unifrac(u_counts, v_counts, otu_ids, tree)
bm[i, j] = uu
bm[j, i] = uu
return bm
def test_unweighted_otus_out_of_order(self):
# UniFrac API does not assert the observations are in tip order of the
# input tree
shuffled_ids = self.oids1[:]
shuffled_b1 = self.b1.copy()
shuffled_ids[0], shuffled_ids[-1] = shuffled_ids[-1], shuffled_ids[0]
shuffled_b1[:, [0, -1]] = shuffled_b1[:, [-1, 0]]
for i in range(len(self.b1)):
for j in range(len(self.b1)):
actual = unweighted_unifrac(self.b1[i], self.b1[j], self.oids1,
self.t1)
expected = unweighted_unifrac(shuffled_b1[i], shuffled_b1[j],
shuffled_ids, self.t1)
self.assertAlmostEqual(actual, expected)
def test_unweighted_otus_out_of_order(self):
# UniFrac API does not assert the observations are in tip order of the
# input tree
shuffled_ids = self.oids1[:]
shuffled_b1 = self.b1.copy()
shuffled_ids[0], shuffled_ids[-1] = shuffled_ids[-1], shuffled_ids[0]
shuffled_b1[:, [0, -1]] = shuffled_b1[:, [-1, 0]]
for i in range(len(self.b1)):
for j in range(len(self.b1)):
actual = unweighted_unifrac(
self.b1[i], self.b1[j], self.oids1, self.t1)
expected = unweighted_unifrac(
shuffled_b1[i], shuffled_b1[j], shuffled_ids, self.t1)
self.assertAlmostEqual(actual, expected)
def test_unweighted_minimal_trees(self):
# two tips
tree = TreeNode.read(StringIO('(OTU1:0.25, OTU2:0.25)root;'))
actual = unweighted_unifrac([1, 0], [0, 0], ['OTU1', 'OTU2'],
tree)
expected = 1.0
self.assertEqual(actual, expected)
def test_unweighted_unifrac_qiime_tiny_test(self):
dm_fp = get_data_path(
os.path.join('qiime-191-tt', 'unweighted_unifrac_dm.txt'), 'data')
expected = DistanceMatrix.read(dm_fp)
for sid1 in self.q_table.columns:
for sid2 in self.q_table.columns:
actual = unweighted_unifrac(
self.q_table[sid1], self.q_table[sid2],
otu_ids=self.q_table.index, tree=self.q_tree)
self.assertAlmostEqual(actual, expected[sid1, sid2])
def test_unweighted_root_not_observed(self):
# expected values computed with QIIME 1.9.1 and by hand
# root node not observed, but branch between (OTU1, OTU2) and root
# is considered shared
actual = unweighted_unifrac([1, 1, 0, 0], [1, 0, 0, 0],
self.oids2, self.t2)
# for clarity of what I'm testing, compute expected as it would
# based on the branch lengths. the values that compose shared was
# a point of confusion for me here, so leaving these in for
# future reference
expected = 0.2 / (0.1 + 0.2 + 0.3) # 0.3333333333
self.assertAlmostEqual(actual, expected)
# root node not observed, but branch between (OTU3, OTU4) and root
# is considered shared
actual = unweighted_unifrac([0, 0, 1, 1], [0, 0, 1, 0],
self.oids2, self.t2)
# for clarity of what I'm testing, compute expected as it would
# based on the branch lengths. the values that compose shared was
# a point of confusion for me here, so leaving these in for
# future reference
expected = 0.7 / (1.1 + 0.5 + 0.7) # 0.3043478261
self.assertAlmostEqual(actual, expected)
def test_unweighted_root_not_observed(self):
# expected values computed with QIIME 1.9.1 and by hand
# root node not observed, but branch between (OTU1, OTU2) and root
# is considered shared
actual = unweighted_unifrac([1, 1, 0, 0], [1, 0, 0, 0], self.oids2,
self.t2)
# for clarity of what I'm testing, compute expected as it would
# based on the branch lengths. the values that compose shared was
# a point of confusion for me here, so leaving these in for
# future reference
expected = 0.2 / (0.1 + 0.2 + 0.3) # 0.3333333333
self.assertAlmostEqual(actual, expected)
# root node not observed, but branch between (OTU3, OTU4) and root
# is considered shared
actual = unweighted_unifrac([0, 0, 1, 1], [0, 0, 1, 0], self.oids2,
self.t2)
# for clarity of what I'm testing, compute expected as it would
# based on the branch lengths. the values that compose shared was
# a point of confusion for me here, so leaving these in for
# future reference
expected = 0.7 / (1.1 + 0.5 + 0.7) # 0.3043478261
self.assertAlmostEqual(actual, expected)
def get_unifrac(
otu_file_1: pathlib.Path,
otu_file_2: pathlib.Path,
tree_file: pathlib.Path,
weighted: bool,
threshold: int,
):
otu_1 = load_table(str(otu_file_1)).to_dataframe(dense=True)
otu_2 = load_table(str(otu_file_2)).to_dataframe(dense=True)
tree = TreeNode.read(str(tree_file))
unifrac_data = dict()
for u, v, otu_ids, col in get_vectors(otu_1, otu_2, threshold):
if weighted:
unifrac_value = weighted_unifrac(
u, v, otu_ids, tree, normalized=True, validate=True
)
else:
unifrac_value = unweighted_unifrac(u, v, otu_ids, tree, validate=True)
unifrac_data[col] = unifrac_value
return pd.Series(unifrac_data), otu_1.shape[0], otu_2.shape[0]
from io import StringIO
from skbio import TreeNode
from skbio.diversity.beta import unweighted_unifrac
tree = TreeNode.read(
StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,'
'(OTU4:0.75,(OTU5:0.5,((OTU6:0.33,OTU7:0.62):0.5'
',OTU8:0.5):0.5):0.5):1.25):0.0)root;'))
u_counts = [1, 0, 0, 4, 1, 2, 3, 0]
v_counts = [0, 1, 1, 6, 0, 1, 0, 0]
otu_ids = ['OTU1', 'OTU2', 'OTU3', 'OTU4', 'OTU5', 'OTU6', 'OTU7', 'OTU8']
uu = unweighted_unifrac(u_counts, v_counts, otu_ids, tree)
print(round(uu, 2))
from ete3 import PhyloTree
t = PhyloTree('((H,I), A, (B,(C,D)))root;', format=1)
print(t)
D = t & "D"
# Get the path from B to the root
node = D
path = []
while node.up:
path.append(node)
node = node.up
# I substract D node from the total number of visited nodes
print("There are", len(path) - 1, "nodes between D and the root")
A = t & "A"
# Get the path from B to the root
node = A
def test_unweighted_unifrac(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# unweighted unifrac implementation
# sample A versus all
actual = unweighted_unifrac(self.b1[0], self.b1[1], self.oids1,
self.t1)
expected = 0.238095238095
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[0], self.b1[2], self.oids1,
self.t1)
expected = 0.52
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[0], self.b1[3], self.oids1,
self.t1)
expected = 0.52
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[0], self.b1[4], self.oids1,
self.t1)
expected = 0.545454545455
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[0], self.b1[5], self.oids1,
self.t1)
expected = 0.619047619048
self.assertAlmostEqual(actual, expected)
# sample B versus remaining
actual = unweighted_unifrac(self.b1[1], self.b1[2], self.oids1,
self.t1)
expected = 0.347826086957
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[1], self.b1[3], self.oids1,
self.t1)
expected = 0.347826086957
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[1], self.b1[4], self.oids1,
self.t1)
expected = 0.68
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[1], self.b1[5], self.oids1,
self.t1)
expected = 0.421052631579
self.assertAlmostEqual(actual, expected)
# sample C versus remaining
actual = unweighted_unifrac(self.b1[2], self.b1[3], self.oids1,
self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[2], self.b1[4], self.oids1,
self.t1)
expected = 0.68
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[2], self.b1[5], self.oids1,
self.t1)
expected = 0.421052631579
self.assertAlmostEqual(actual, expected)
# sample D versus remaining
actual = unweighted_unifrac(self.b1[3], self.b1[4], self.oids1,
self.t1)
expected = 0.68
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(self.b1[3], self.b1[5], self.oids1,
self.t1)
expected = 0.421052631579
self.assertAlmostEqual(actual, expected)
# sample E versus remaining
actual = unweighted_unifrac(self.b1[4], self.b1[5], self.oids1,
self.t1)
expected = 1.0
self.assertAlmostEqual(actual, expected)
def test_unweighted_unifrac_identity(self):
for i in range(len(self.b1)):
actual = unweighted_unifrac(self.b1[i], self.b1[i], self.oids1,
self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
def test_unweighted_unifrac(self):
# expected results derived from QIIME 1.9.1, which
# is a completely different implementation skbio's initial
# unweighted unifrac implementation
# sample A versus all
actual = unweighted_unifrac(
self.table1[0], self.table1[1], self.oids1, self.t1)
expected = 0.238095238095
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[0], self.table1[2], self.oids1, self.t1)
expected = 0.52
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[0], self.table1[3], self.oids1, self.t1)
expected = 0.52
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[0], self.table1[4], self.oids1, self.t1)
expected = 0.545454545455
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[0], self.table1[5], self.oids1, self.t1)
expected = 0.619047619048
self.assertAlmostEqual(actual, expected)
# sample B versus remaining
actual = unweighted_unifrac(
self.table1[1], self.table1[2], self.oids1, self.t1)
expected = 0.347826086957
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[1], self.table1[3], self.oids1, self.t1)
expected = 0.347826086957
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[1], self.table1[4], self.oids1, self.t1)
expected = 0.68
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[1], self.table1[5], self.oids1, self.t1)
expected = 0.421052631579
self.assertAlmostEqual(actual, expected)
# sample C versus remaining
actual = unweighted_unifrac(
self.table1[2], self.table1[3], self.oids1, self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[2], self.table1[4], self.oids1, self.t1)
expected = 0.68
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[2], self.table1[5], self.oids1, self.t1)
expected = 0.421052631579
self.assertAlmostEqual(actual, expected)
# sample D versus remaining
actual = unweighted_unifrac(
self.table1[3], self.table1[4], self.oids1, self.t1)
expected = 0.68
self.assertAlmostEqual(actual, expected)
actual = unweighted_unifrac(
self.table1[3], self.table1[5], self.oids1, self.t1)
expected = 0.421052631579
self.assertAlmostEqual(actual, expected)
# sample E versus remaining
actual = unweighted_unifrac(
self.table1[4], self.table1[5], self.oids1, self.t1)
expected = 1.0
self.assertAlmostEqual(actual, expected)
def test_unweighted_unifrac_kwargs(self):
# confirm that **kwargs can be passed
actual = unweighted_unifrac(self.table1[0], self.table1[0], self.oids1,
self.t1, not_a_known_parameter=42)
self.assertAlmostEqual(actual, 0.0)
def test_unweighted_unifrac_identity(self):
for i in range(len(self.table1)):
actual = unweighted_unifrac(
self.table1[i], self.table1[i], self.oids1, self.t1)
expected = 0.0
self.assertAlmostEqual(actual, expected)