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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# ----------------------------------------------------------------------------
from unittest import TestCase, main
from io import StringIO
import os
import numpy as np
import pandas as pd
from skbio import TreeNode
from skbio.util import get_data_path
from skbio.tree import DuplicateNodeError, MissingNodeError
from skbio.diversity.alpha import faith_pd, phydiv
class FaithPDTests(TestCase):
def setUp(self):
self.counts = np.array([0, 1, 1, 4, 2, 5, 2, 4, 1, 2])
self.b1 = np.array([[1, 3, 0, 1, 0],
[0, 2, 0, 4, 4],
[0, 0, 6, 2, 1],
[0, 0, 1, 1, 1],
[2, 0, 3, 0, 0]])
self.sids1 = list('ABCDE')
self.oids1 = ['OTU%d' % i for i in range(1, 6)]
self.t1 = TreeNode.read(StringIO(
'(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):'
'0.0,(OTU4:0.75,OTU5:0.75):1.25):0.0)root;'))
self.t1_w_extra_tips = TreeNode.read(
StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
'0.75,(OTU5:0.25,(OTU6:0.5,OTU7:0.5):0.5):0.5):1.25):0.0'
')root;'))
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)
actual = faith_pd(self.b1[4], self.oids1, self.t1)
expected = 3.0
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)
actual = faith_pd(self.b1[4], self.oids1, self.t1_w_extra_tips)
expected = 3.0
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_one_observed(self):
actual = faith_pd([1, 0, 0, 0, 0], self.oids1, self.t1)
expected = 2.0
self.assertAlmostEqual(actual, expected)
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_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],
taxa=self.q_table.index,
tree=self.q_tree)
self.assertAlmostEqual(actual, expected['PD_whole_tree'][sid])
def test_faith_pd_root_not_observed(self):
# expected values computed by hand
tree = TreeNode.read(
StringIO('((OTU1:0.1, OTU2:0.2):0.3, (OTU3:0.5, OTU4:0.7):1.1)'
'root;'))
taxa = ['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], taxa, 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], taxa, tree)
expected = 2.3
self.assertAlmostEqual(actual, expected)
def test_faith_pd_invalid_input(self):
# tree has duplicated tip ids
t = TreeNode.read(
StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
'0.75,OTU2:0.75):1.25):0.0)root;'))
counts = [1, 2, 3]
taxa = ['OTU1', 'OTU2', 'OTU3']
self.assertRaises(DuplicateNodeError, faith_pd, counts, taxa,
t)
# unrooted tree as input
t = TreeNode.read(StringIO('((OTU1:0.1, OTU2:0.2):0.3, OTU3:0.5,'
'OTU4:0.7);'))
counts = [1, 2, 3]
taxa = ['OTU1', 'OTU2', 'OTU3']
self.assertRaises(ValueError, faith_pd, counts, taxa, t)
# taxa has duplicated ids
t = TreeNode.read(
StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
'0.75,OTU5:0.75):1.25):0.0)root;'))
counts = [1, 2, 3]
taxa = ['OTU1', 'OTU2', 'OTU2']
self.assertRaises(ValueError, faith_pd, counts, taxa, t)
# len of vectors not equal
t = TreeNode.read(
StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
'0.75,OTU5:0.75):1.25):0.0)root;'))
counts = [1, 2]
taxa = ['OTU1', 'OTU2', 'OTU3']
self.assertRaises(ValueError, faith_pd, counts, taxa, t)
counts = [1, 2, 3]
taxa = ['OTU1', 'OTU2']
self.assertRaises(ValueError, faith_pd, counts, taxa, t)
# negative counts
t = TreeNode.read(
StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
'0.75,OTU5:0.75):1.25):0.0)root;'))
counts = [1, 2, -3]
taxa = ['OTU1', 'OTU2', 'OTU3']
self.assertRaises(ValueError, faith_pd, counts, taxa, t)
# tree with no branch lengths
t = TreeNode.read(
StringIO('((((OTU1,OTU2),OTU3)),(OTU4,OTU5));'))
counts = [1, 2, 3]
taxa = ['OTU1', 'OTU2', 'OTU3']
self.assertRaises(ValueError, faith_pd, counts, taxa, t)
# tree missing some branch lengths
t = TreeNode.read(
StringIO('(((((OTU1,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
'0.75,OTU5:0.75):1.25):0.0)root;'))
counts = [1, 2, 3]
taxa = ['OTU1', 'OTU2', 'OTU3']
self.assertRaises(ValueError, faith_pd, counts, taxa, t)
# taxa not present in tree
t = TreeNode.read(
StringIO('(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:'
'0.75,OTU5:0.75):1.25):0.0)root;'))
counts = [1, 2, 3]
taxa = ['OTU1', 'OTU2', 'OTU42']
self.assertRaises(MissingNodeError, faith_pd, counts, taxa, t)
class PhyDivTests(TestCase):
def setUp(self):
self.tree = TreeNode.read(StringIO(
'(((a:0.4,b:0.5):0.7,((c:0.1,d:0.2):0.6,(e:0.2,f:0.3):0.4):0.2)'
':0.1,g:1.2):0.2;'))
# each dash (-) represents branch length = 0.05
#
# /--------a
# /--------------|
# | \----------b
# |
# /--| /--c
# | | /------------|
# | | | \----d
# | \----|
# ----| | /----e
# | \--------|
# | \------f
# |
# \------------------------g
self.taxa = list('abcdef')
self.data = np.array([
[1, 2, 0, 0, 0, 0], # clade (a, b)
[0, 0, 3, 4, 0, 0], # clade (c, d)
[0, 0, 0, 0, 5, 6], # clade (e, f)
[0, 0, 3, 4, 5, 6], # non-basal, monophyletic group (c, d, e, f)
[1, 2, 3, 4, 0, 0]]) # basal, non-monophyletic group (a, b, c, d)
def test_phydiv_rooted_unweighted(self):
# equivalent to faith_pd
for datum in self.data:
obs = phydiv(datum, self.taxa, self.tree)
exp = faith_pd(datum, self.taxa, self.tree)
self.assertAlmostEqual(obs, exp)
def test_phydiv_unrooted_unweighted(self):
# equivalent to faith_pd without path to root
exps = [0.9, 0.3, 0.5, 1.8, 2.7]
for datum, exp in zip(self.data, exps):
obs = phydiv(datum, self.taxa, self.tree, rooted=False)
self.assertAlmostEqual(obs, exp)
# edge case: one taxon
obs = phydiv([1], ['a'], self.tree, rooted=False)
self.assertEqual(obs, 0)
# edge case: zero taxon
obs = phydiv([0], ['a'], self.tree, rooted=False)
self.assertEqual(obs, 0)
# edge case: no taxon
obs = phydiv([], [], self.tree, rooted=False)
self.assertEqual(obs, 0)
def test_phydiv_rooted_weighted(self):
# group (a, b)
# = (0.4 * 1 + 0.5 * 2 + (0.7 + 0.1 + 0.2) * (1 + 2)) / (1 + 2)
obs = phydiv(self.data[0], self.taxa, self.tree, weight=True)
exp = 1.46666667
self.assertAlmostEqual(obs, exp)
# group (c, d)
# = (0.1 * 3 + 0.2 * 4 + (0.6 + 0.2 + 0.1 + 0.2) * (3 + 4)) / (3 + 4)
obs = phydiv(self.data[1], self.taxa, self.tree, weight=True)
exp = 1.25714286
self.assertAlmostEqual(obs, exp)
# group (c, d, e, f)
# = (0.1 * 3 + 0.2 * 4 + 0.2 * 5 + 0.3 * 6 + 0.6 * (3 + 4) + 0.4 *
# (5 + 6) + (0.2 + 0.1 + 0.2) * (3 + 4 + 5 + 6)) / (3 + 4 + 5 + 6)
obs = phydiv(self.data[3], self.taxa, self.tree, weight=True)
exp = 1.19444444
self.assertAlmostEqual(obs, exp)
# group (a, b, c, d)
# = (0.4 * 1 + 0.5 * 2 + 0.1 * 3 + 0.2 * 4 + 0.7 * (1 + 2) + (0.6 +
# 0.2) * (3 + 4) + (0.1 + 0.2) * (1 + 2 + 3 + 4)) / (1 + 2 + 3 + 4)
obs = phydiv(self.data[4], self.taxa, self.tree, weight=True)
exp = 1.32
self.assertAlmostEqual(obs, exp)
def test_phydiv_unrooted_weighted(self):
# a.k.a., balance-weighted PD
# group (a, b)
# = (0.4 + 0.5) * 2 * min(1, 2) / (1 + 2)
obs = phydiv(self.data[0], self.taxa, self.tree,
rooted=False, weight=True)
exp = 0.6
self.assertAlmostEqual(obs, exp)
# group (c, d)
# = (0.1 + 0.2) * 2 * min(3, 4) / (3 + 4)
obs = phydiv(self.data[1], self.taxa, self.tree,
rooted=False, weight=True)
exp = 0.25714286
self.assertAlmostEqual(obs, exp)
# group (c, d, e, f)
# = 2 * (0.1 * min(3, 4 + 5 + 6) + 0.2 * min(4, 3 + 5 + 6) + 0.2 *
# min(5, 3 + 4 + 6) + 0.3 * min(6, 3 + 4 + 5) + (0.6 + 0.4) *
# min(3 + 4, 5 + 6)) / (3 + 4 + 5 + 6)
obs = phydiv(self.data[3], self.taxa, self.tree,
rooted=False, weight=True)
exp = 1.21111111
self.assertAlmostEqual(obs, exp)
# group (a, b, c, d)
# = 2 * (0.4 * min(1, 2 + 3 + 4) + 0.5 * min(2, 1 + 3 + 4) + (0.7 +
# 0.6 + 0.2) * min(1 + 2, 3 + 4) + 0.1 * min(3, 1 + 2 + 4) + 0.2 *
# min(4, 1 + 2 + 3)) / (1 + 2 + 3 + 4)
obs = phydiv(self.data[4], self.taxa, self.tree,
rooted=False, weight=True)
exp = 1.4
self.assertAlmostEqual(obs, exp)
# edge cases
self.assertEqual(phydiv([1], ['a'], self.tree, False, True), 0)
self.assertEqual(phydiv([0], ['a'], self.tree, False, True), 0)
self.assertEqual(phydiv([], [], self.tree, False, True), 0)
def test_phydiv_weight_param(self):
# group (a, b), unrooted
# = (0.4 + 0.5) * (2 * min(1, 2) / (1 + 2)) ** theta
obs = phydiv(self.data[0], self.taxa, self.tree, False, 0.5)
exp = 0.73484692
self.assertAlmostEqual(obs, exp)
obs = phydiv(self.data[0], self.taxa, self.tree, False, 0.25)
exp = 0.81324180
self.assertAlmostEqual(obs, exp)
# fall back to unweighted
obs = phydiv(self.data[0], self.taxa, self.tree, False, 0)
exp = 0.9
# fall back to fully-weighted
self.assertAlmostEqual(obs, exp)
obs = phydiv(self.data[0], self.taxa, self.tree, False, 1)
exp = 0.6
self.assertAlmostEqual(obs, exp)
# rooted
# = (0.4 * 1 ** theta + 0.5 * 2 ** theta + (0.7 + 0.1 + 0.2) *
# (1 + 2) ** theta) / (1 + 2) ** theta
obs = phydiv(self.data[0], self.taxa, self.tree, True, 0.5)
exp = 1.63918840
self.assertAlmostEqual(obs, exp)
obs = phydiv(self.data[0], self.taxa, self.tree, True, 0.25)
exp = 1.75573528
self.assertAlmostEqual(obs, exp)
# edge cases
self.assertEqual(phydiv([1], ['a'], self.tree, False, 0.5), 0)
self.assertEqual(phydiv([0], ['a'], self.tree, False, 0.5), 0)
self.assertEqual(phydiv([], [], self.tree, False, 0.5), 0)
def test_phydiv_tree_unrooted(self):
# convert tree to unrooted
outgroup = self.tree.find('g')
ingroup = outgroup.siblings()[0]
unrooted = ingroup.copy()
unrooted.extend([outgroup.copy()])
unrooted.length += self.tree.length or 0.0
# auto-enter unrooted mode
obs = phydiv(self.data[0], self.taxa, unrooted)
exp = phydiv(self.data[0], self.taxa, self.tree, rooted=False)
self.assertEqual(obs, exp)
# force rooted mode
obs = phydiv(self.data[0], self.taxa, unrooted, rooted=True)
exp = phydiv(self.data[0], self.taxa, self.tree)
self.assertEqual(obs, exp)
def test_phydiv_invalid_weight(self):
params = (self.data[0], self.taxa, self.tree)
self.assertRaises(ValueError, phydiv, *params, weight='hello')
self.assertRaises(ValueError, phydiv, *params, weight=-0.5)
self.assertRaises(ValueError, phydiv, *params, weight=2.0)
if __name__ == "__main__":
main()
|
