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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, BP development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
# line length is useful here, so disabling check
# flake8: noqa: E501
from unittest import TestCase, main
import numpy as np
import numpy.testing as npt
from bp import BP, parse_newick
import bp.tests.test_bp_cy as tbc
for name in dir(tbc):
if name.startswith('test_'):
getattr(tbc, name)()
class BPTests(TestCase):
def setUp(self):
# 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
self.fig1_B = np.array([1, 1, 1, 0, 1, 0, 1, 1 ,0, 0, 0, 1, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0], dtype=np.uint8)
self.BP = BP(self.fig1_B)
def test_rmq(self):
# ( ( ( ) ( ) ( ( ) ) ) ( ) ( ( ( ) ( ) ) ) )
#excess 1 2 3 2 3 2 3 4 3 2 1 2 1 2 3 4 3 4 3 2 1 0
#i 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
exp = [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 21],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[2, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[4, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[6, 6, 6, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[7, 8, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[8, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21],
[11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21],
[12, 12, 12, 12, 12, 12, 12, 12, 12, 21],
[13, 13, 13, 13, 13, 13, 13, 20, 21],
[14, 14, 14, 14, 14, 19, 20, 21],
[15, 16, 16, 16, 19, 20, 21],
[16, 16, 16, 19, 20, 21],
[17, 18, 19, 20, 21],
[18, 19, 20, 21],
[19, 20, 21],
[20, 21],
[21]]
for i in range(len(self.fig1_B)):
for j in range(i+1, len(self.fig1_B)):
self.assertEqual(self.BP.rmq(i, j), exp[i][j - i])
def test_rMq(self):
# ( ( ( ) ( ) ( ( ) ) ) ( ) ( ( ( ) ( ) ) ) )
#excess 1 2 3 2 3 2 3 4 3 2 1 2 1 2 3 4 3 4 3 2 1 0
#i 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
exp = [[0, 1, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7],
[1, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7],
[2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7],
[3, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7],
[4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7],
[5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7],
[6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7],
[7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7],
[8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15],
[9, 9, 9, 9, 9, 14, 15, 15, 15, 15, 15, 15, 15],
[10, 11, 11, 11, 14, 15, 15, 15, 15, 15, 15, 15],
[11, 11, 11, 14, 15, 15, 15, 15, 15, 15, 15],
[12, 13, 14, 15, 15, 15, 15, 15, 15, 15],
[13, 14, 15, 15, 15, 15, 15, 15, 15],
[14, 15, 15, 15, 15, 15, 15, 15],
[15, 15, 15, 15, 15, 15, 15],
[16, 17, 17, 17, 17, 17],
[17, 17, 17, 17, 17],
[18, 18, 18, 18],
[19, 19, 19],
[20, 20],
[21]]
for i in range(len(self.fig1_B)):
for j in range(i+1, len(self.fig1_B)):
self.assertEqual(self.BP.rMq(i, j), exp[i][j - i])
def test_mincount(self):
# ( ( ( ) ( ) ( ( ) ) ) ( ) ( ( ( ) ( ) ) ) )
#i 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
#excess 1 2 3 2 3 2 3 4 3 2 1 2 1 2 3 4 3 4 3 2 1 0
exp = [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 1],
[1, 1, 2, 2, 3, 3, 3, 3, 4, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 1, 2, 2, 2, 2, 3, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 2, 2, 2, 2, 3, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 1, 1, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 1, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 2, 1],
[1, 1, 1, 1, 1, 1, 2, 1, 1],
[1, 1, 2, 2, 3, 1, 1, 1],
[1, 1, 1, 2, 1, 1, 1],
[1, 1, 2, 1, 1, 1],
[1, 1, 1, 1, 1],
[1, 1, 1, 1],
[1, 1, 1],
[1, 1],
[1]]
for i in range(len(self.fig1_B)):
for j in range(i+1, len(self.fig1_B)):
self.assertEqual(self.BP.mincount(i, j), exp[i][j - i])
def test_minselect(self):
"""position of the qth minimum in excess(i), excess(i + 1), . . . , excess(j)."""
exp = {(0, 20, 1): 0,
(0, 21, 1): 21,
(0, 20, 2): 10,
(0, 21, 2): None,
(0, 20, 3): 12,
(0, 20, 4): 20,
(8, 15, 1): 10,
(8, 15, 2): 12,
(6, 9, 1): 9}
for (i, j, q), e in exp.items():
self.assertEqual(self.BP.minselect(i, j, q), e)
def test_preorder(self):
exp = [1, 2, 3, 3, 4, 4, 5, 6, 6, 5, 2, 7, 7, 8, 9, 10, 10, 11, 11, 9, 8, 1]
for i, e in enumerate(exp):
self.assertEqual(self.BP.preorder(i), e)
def test_preorderselect(self):
exp = [0, 1, 2, 4, 6, 7, 11, 13, 14, 15, 17]
for k, e in enumerate(exp):
self.assertEqual(self.BP.preorderselect(k), e)
def test_postorder(self):
exp = [11, 5, 1, 1, 2, 2, 4, 3, 3, 4, 5, 6, 6, 10, 9, 7, 7, 8, 8, 9, 10, 11]
for i, e in enumerate(exp):
self.assertEqual(self.BP.postorder(i), e)
def test_postorderselect(self):
exp = [2, 4, 7, 6, 1, 11, 15, 17, 14, 13, 0]
for k, e in enumerate(exp):
self.assertEqual(self.BP.postorderselect(k + 1), e)
def test_isancestor(self):
exp = {(0, 0): False, # identity test
(2, 1): False, # tip test
(1, 2): True, # open test
(1, 3): True, # close test
(0, 7): True, # nested test
(1, 7): True} # nested test
for (i, j), e in exp.items():
self.assertEqual(self.BP.isancestor(i, j), e)
def test_subtree(self):
exp = [11, 5, 1, 1, 1, 1, 2, 1, 1, 2, 5, 1, 1, 4, 3, 1, 1, 1, 1, 3, 4, 11]
for i, e in enumerate(exp):
self.assertEqual(self.BP.subtree(i), e)
def test_levelancestor(self):
exp = {(2, 1): 1, # first tip to its parent
(2, 2): 0, # first tip to root
(4, 1): 1, # second tip to its parent
(5, 1): 1, # second tip, closing, to its parent
(7, 1): 6, # deep tip to its parent
(7, 2): 1, # deep tip to its grandparent
(7, 3): 0, # deep tip to its great grand parent
(7, 9999): 0, # max out at the root
(10, 0): -1} # can't be an ancestor of yourself
for (i, d), e in exp.items():
self.assertEqual(self.BP.levelancestor(i, d), e)
def _testinator(self, exp, f, verbose=False):
self.assertEqual(len(exp), len(self.fig1_B))
for i, e in enumerate(exp):
if verbose:
print(i, e)
self.assertEqual(f(i), e)
def test_levelnext(self):
# ( ( ( ) ( ) ( ( ) ) ) ( ) ( ( ( ) ( ) ) ) )
exp = [-1, 11, 4, 4, 6, 6, 14, 15, 15, 14, 11, 13, 13, -1, -1, 17, 17, -1, -1, -1, -1, -1]
self.assertEqual(len(exp), len(self.fig1_B))
for i, e in enumerate(exp):
self.assertEqual(self.BP.levelnext(i), e)
def test_close(self):
exp = [21, 10, 3, 5, 9, 8, 12, 20, 19, 16, 18]
for i, e in zip(np.argwhere(self.BP.B == 1).squeeze(), exp):
npt.assert_equal(self.BP.close(i), e)
def test_lca(self):
# lca(i, j) = parent(rmq(i, j) + 1)
# unless isancestor(i, j)
# (so lca(i, j) = i) or isancestor(j, i) (so lca(i, j) = j),
nodes = [self.BP.preorderselect(k) for k in range(self.fig1_B.sum())]
exp = {(nodes[2], nodes[3]): nodes[1],
(nodes[2], nodes[5]): nodes[1],
(nodes[2], nodes[9]): nodes[0],
(nodes[9], nodes[10]): nodes[8],
(nodes[1], nodes[8]): nodes[0]}
for (i, j), e in exp.items():
self.assertEqual(self.BP.lca(i, j), e)
def test_deepestnode(self):
# deepestnode(i) = rMq(i, close(i)),
exp = [7, 7, 2, 2, 4, 4, 7, 7, 7, 7, 7, 11, 11, 15, 15, 15, 15, 17, 17, 15, 15, 7]
self._testinator(exp, self.BP.deepestnode)
def test_height(self):
# height(i) = excess(deepestnode(i)) − excess(i).
exp = [3, 2, 0, 0, 0, 0, 1, 0, 0, 1, 2, 0, 0, 2, 1, 0, 0, 0, 0, 1, 2, 3]
self._testinator(exp, self.BP.height)
def test_ntips(self):
exp = 6
obs = self.BP.ntips()
self.assertEqual(obs, exp)
def test_shear(self):
# r 2 3 4 5 6 7 8 9 10 11
# ( ( ( ) ( ) ( ( ) ) ) ( ) ( ( ( ) ( ) ) ) )
#i 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
names = np.array(['r', '2', '3', None, '4', None, '5', '6', None, None, None, '7', None, '8', '9', '10', None,
'11', None, None, None, None])
lengths = np.array([0, 1, 2, 0, 3, 0, 4, 5, 0, 0, 0, 6, 0, 7, 8, 9, 0, 10, 0, 0, 0, 0], dtype=np.double)
self.BP.set_names(names)
self.BP.set_lengths(lengths)
in_ = {'4', '6', '7', '10', '11'}
exp = np.array([1, 1, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 1, 0, 0,
0, 0], dtype=np.uint32)
exp_n = np.array(['r', '2', '4', None, '5', '6', None, None, None, '7', None, '8', '9', '10', None, '11', None,
None, None, None])
exp_l = np.array([0, 1, 3, 0, 4, 5, 0, 0, 0, 6, 0, 7, 8, 9, 0, 10, 0, 0, 0, 0], dtype=np.double)
obs = self.BP.shear(in_)
npt.assert_equal(exp, obs.B)
for i in range(len(obs.B)):
self.assertEqual(obs.name(i), exp_n[i])
self.assertEqual(obs.length(i), exp_l[i])
in_ = {'10', '11'}
exp = np.array([1, 1, 1, 1, 0, 1, 0, 0, 0, 0], dtype=np.uint32)
obs = self.BP.shear(in_).B
npt.assert_equal(obs, exp)
def test_shear_raise_tree_is_empty(self):
names = np.array(['r', '2', '3', None, '4', None, '5', '6', None, None, None, '7', None, '8', '9', '10', None,
'11', None, None, None, None])
lengths = np.array([0, 1, 2, 0, 3, 0, 4, 5, 0, 0, 0, 6, 0, 7, 8, 9, 0, 10, 0, 0, 0, 0], dtype=np.double)
self.BP.set_names(names)
with self.assertRaises(ValueError):
self.BP.shear({'not', 'in', 'tree'})
def test_collapse(self):
names = np.array(['r', '2', '3', None, '4', None, '5', '6', None, None, None, '7', None, '8', '9', '10', None,
'11', None, None, None, None])
lengths = np.array([0, 1, 2, 0, 3, 0, 4, 5, 0, 0, 0, 6, 0, 7, 8, 9, 0, 10, 0, 0, 0, 0], dtype=np.double)
self.BP.set_names(names)
self.BP.set_lengths(lengths)
exp = np.array([1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0],
dtype=np.uint8)
exp_n = ['r', '2', '3', None, '4', None, '6', None, None, '7', None, '9', '10', None, '11', None, None, None]
exp_l = [0, 1, 2, 0, 3, 0, 9, 0, 0, 6, 0, 15, 9, 0, 10, 0, 0, 0]
obs = self.BP.collapse()
npt.assert_equal(obs.B, exp)
for i in range(len(obs.B)):
self.assertEqual(obs.name(i), exp_n[i])
self.assertEqual(obs.length(i), exp_l[i])
bp = BP(np.array([1, 1, 1, 0, 0, 1, 0, 0], dtype=np.uint8))
exp = np.array([1, 1, 0, 1, 0, 0])
obs = bp.collapse().B
npt.assert_equal(obs, exp)
def test_name_unset(self):
for i in range(self.BP.B.size):
self.assertEqual(self.BP.name(i), None)
def test_length_unset(self):
for i in range(self.BP.B.size):
self.assertEqual(self.BP.length(i), 0.0)
def test_name_length_set(self):
names = np.full(self.BP.B.size, None, dtype=object)
lengths = np.zeros(self.BP.B.size, dtype=np.double)
names[0] = 'root'
names[self.BP.preorderselect(7)] = 'other'
lengths[1] = 1.23
lengths[self.BP.preorderselect(5)] = 5.43
self.BP.set_names(names)
self.BP.set_lengths(lengths)
self.assertEqual(self.BP.name(0), 'root')
self.assertEqual(self.BP.name(1), None)
self.assertEqual(self.BP.name(13), 'other')
self.assertEqual(self.BP.length(1), 1.23)
self.assertEqual(self.BP.length(5), 0.0)
self.assertEqual(self.BP.length(7), 5.43)
if __name__ == '__main__':
main()
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