def test_exhaustive(self):
# check if execution is rejected if number of combination is too high
self.assertRaisesRegex(
RuntimeError,
'Cowardly refuse to test ',
prototype_selection_exhaustive,
self.dm20,
5,
max_combinations_to_test=1000)
self.assertRaisesRegex(
ValueError,
"must be >= 2, since a single",
prototype_selection_exhaustive,
self.dm20,
1)
self.assertRaisesRegex(
ValueError,
"otherwise no reduction is necessary",
prototype_selection_exhaustive,
self.dm20,
len(self.dm20.ids)+1)
res = prototype_selection_exhaustive(self.dm20, 3)
self.assertCountEqual(('A', 'P', 'Q'), res)
self.assertAlmostEqual(1.841, distance_sum(res, self.dm20))
res = prototype_selection_exhaustive(self.dm20, 4)
self.assertCountEqual(('A', 'J', 'P', 'T'), res)
self.assertAlmostEqual(3.4347, distance_sum(res, self.dm20))
res = prototype_selection_exhaustive(self.dm20, 5)
self.assertCountEqual(('A', 'C', 'O', 'P', 'T'), res)
self.assertAlmostEqual(5.4494, distance_sum(res, self.dm20))
res = prototype_selection_exhaustive(self.dm20, 18)
self.assertCountEqual(
('A', 'B', 'C', 'D', 'E', 'F', 'G', 'I', 'J', 'K', 'L', 'M', 'N',
'O', 'P', 'Q', 'R', 'T'),
res)
self.assertAlmostEqual(66.94, distance_sum(res, self.dm20))
res = prototype_selection_exhaustive(self.dm20, 19)
self.assertCountEqual(
('A', 'B', 'C', 'D', 'E', 'F', 'G', 'I', 'J', 'K', 'L', 'M', 'N',
'O', 'P', 'Q', 'R', 'S', 'T'),
res)
self.assertAlmostEqual(74.1234, distance_sum(res, self.dm20))
def test_distance_sum(self):
# test that no missing IDs can be used
self.assertRaisesRegex(
MissingIDError,
'The ID \'X\' is not in the dissimilarity matrix.',
distance_sum,
['A', 'B', 'X'],
self.dm20)
# test that no ID is duplicated
self.assertRaisesRegex(
DissimilarityMatrixError,
'IDs must be unique. Found the following duplicate IDs',
distance_sum,
['A', 'B', 'C', 'D', 'B'],
self.dm20)
# test that list of IDs holds at least 1 element
self.assertRaisesRegex(
DissimilarityMatrixError,
'Data must be at least 1x1 in size',
distance_sum,
[],
self.dm20)
# test for result correctness
self.assertAlmostEqual(2454.1437464961, distance_sum(self.dm100.ids,
self.dm100))
self.assertAlmostEqual(32.9720926186, distance_sum(
['550.L1S173.s.1.sequence', '550.L1S141.s.1.sequence',
'550.L1S18.s.1.sequence', '550.L1S156.s.1.sequence',
'550.L1S110.s.1.sequence', '550.L1S143.s.1.sequence',
'550.L1S134.s.1.sequence', '550.L1S103.s.1.sequence',
'550.L1S185.s.1.sequence', '550.L1S114.s.1.sequence',
'550.L1S138.s.1.sequence', '550.L1S137.s.1.sequence'],
self.dm100))
self.assertAlmostEqual(81.6313, distance_sum(self.dm20.ids,
self.dm20))
self.assertAlmostEqual(13.3887, distance_sum(
['A', 'C', 'F', 'G', 'M', 'N', 'P', 'T'],
self.dm20))
def test_seedset(self):
# test seedset function, first include elements that are supposed to
# be selected, to see if result is identical
seedset = set(['A', 'P'])
res = prototype_selection_exhaustive(self.dm20, 5, seedset)
self.assertCountEqual(('A', 'P', 'T', 'C', 'O'), res)
self.assertAlmostEqual(5.4494, distance_sum(res, self.dm20))
seedset = set(['A', 'P'])
res = prototype_selection_constructive_maxdist(self.dm20, 5, seedset)
self.assertCountEqual(('A', 'P', 'Q', 'C', 'O'), res)
self.assertAlmostEqual(5.4480, distance_sum(res, self.dm20))
seedset = set(['A', 'H'])
res = prototype_selection_constructive_pMedian(self.dm20, 5, seedset)
self.assertCountEqual(('A', 'H', 'Q', 'E', 'I'), res)
self.assertAlmostEqual(5.1449, distance_sum(res, self.dm20))
seedset = set(['A', 'P'])
res = prototype_selection_destructive_maxdist(self.dm20, 5, seedset)
self.assertCountEqual(('A', 'P', 'T', 'C', 'O'), res)
self.assertAlmostEqual(5.4494, distance_sum(res, self.dm20))
seedset = set(['H', 'C'])
res = prototype_selection_constructive_protoclass(
self.dm20, 5, seedset=seedset)
self.assertCountEqual(('H', 'C', 'Q', 'A', 'G'), res)
self.assertAlmostEqual(5.2747, distance_sum(res, self.dm20))
# then include different elements, to see result changes, and score
# (sum of distances) slightly drops.
seedset = ['G', 'I']
res = prototype_selection_exhaustive(self.dm20, 5, seedset)
self.assertCountEqual(('A', 'G', 'I', 'C', 'T'), res)
self.assertAlmostEqual(5.3091, distance_sum(res, self.dm20))
seedset = ['G', 'I']
res = prototype_selection_constructive_maxdist(self.dm20, 5, seedset)
self.assertCountEqual(('A', 'G', 'I', 'C', 'T'), res)
self.assertAlmostEqual(5.3091, distance_sum(res, self.dm20))
seedset = ['G', 'T']
res = prototype_selection_constructive_pMedian(self.dm20, 5, seedset)
self.assertCountEqual(('A', 'G', 'E', 'H', 'T'), res)
self.assertAlmostEqual(5.2263, distance_sum(res, self.dm20))
seedset = ['G', 'I']
res = prototype_selection_destructive_maxdist(self.dm20, 5, seedset)
self.assertCountEqual(('A', 'G', 'I', 'K', 'T'), res)
self.assertAlmostEqual(5.3082, distance_sum(res, self.dm20))
seedset = set(['G', 'I'])
res = prototype_selection_constructive_protoclass(
self.dm20, 5, seedset=seedset)
self.assertCountEqual(('I', 'G', 'B', 'Q', 'A'), res)
self.assertAlmostEqual(5.1918, distance_sum(res, self.dm20))
# test on the n=100 distance matrix
seedset = ['550.L1S18.s.1.sequence', '550.L1S142.s.1.sequence',
'550.L1S176.s.1.sequence']
res = prototype_selection_constructive_maxdist(self.dm100, 10, seedset)
self.assertCountEqual(
('550.L1S1.s.1.sequence', '550.L1S15.s.1.sequence',
'550.L1S18.s.1.sequence', '550.L1S129.s.1.sequence',
'550.L1S115.s.1.sequence', '550.L1S136.s.1.sequence',
'550.L1S142.s.1.sequence', '550.L1S176.s.1.sequence',
'550.L1S178.s.1.sequence', '550.L1S189.s.1.sequence'),
res)
self.assertAlmostEqual(26.7929168423, distance_sum(res, self.dm100))
res = prototype_selection_constructive_pMedian(self.dm100, 10, seedset)
self.assertCountEqual(
('550.L1S117.s.1.sequence', '550.L1S18.s.1.sequence',
'550.L1S12.s.1.sequence', '550.L1S163.s.1.sequence',
'550.L1S149.s.1.sequence', '550.L1S185.s.1.sequence',
'550.L1S133.s.1.sequence', '550.L1S126.s.1.sequence',
'550.L1S176.s.1.sequence', '550.L1S142.s.1.sequence'),
res)
self.assertAlmostEqual(23.9872385276, distance_sum(res, self.dm100))
res = prototype_selection_destructive_maxdist(self.dm100, 10, seedset)
self.assertCountEqual(
('550.L1S1.s.1.sequence', '550.L1S15.s.1.sequence',
'550.L1S18.s.1.sequence', '550.L1S129.s.1.sequence',
'550.L1S132.s.1.sequence', '550.L1S136.s.1.sequence',
'550.L1S142.s.1.sequence', '550.L1S147.s.1.sequence',
'550.L1S176.s.1.sequence', '550.L1S189.s.1.sequence'),
res)
self.assertAlmostEqual(26.7457727563, distance_sum(res, self.dm100))
def test_prototype_selection_constructive_pMedian(self):
self.assertRaisesRegex(
ValueError,
"must be >= 2, since a single",
prototype_selection_constructive_pMedian,
self.dm20,
1)
self.assertRaisesRegex(
ValueError,
"otherwise no reduction is necessary",
prototype_selection_constructive_pMedian,
self.dm20,
len(self.dm20.ids)+1)
res = prototype_selection_constructive_pMedian(self.dm20, 3)
self.assertCountEqual(('A', 'H', 'Q'), res)
self.assertAlmostEqual(1.7387, distance_sum(res, self.dm20))
res = prototype_selection_constructive_pMedian(self.dm20, 4)
self.assertCountEqual(('A', 'H', 'Q', 'E'), res)
self.assertAlmostEqual(3.2306, distance_sum(res, self.dm20))
res = prototype_selection_constructive_pMedian(self.dm20, 5)
self.assertCountEqual(('A', 'H', 'Q', 'E', 'I'), res)
self.assertAlmostEqual(5.1449, distance_sum(res, self.dm20))
res = prototype_selection_constructive_pMedian(self.dm20, 18)
self.assertCountEqual(
('A', 'B', 'C', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T'),
res)
self.assertAlmostEqual(66.4087, distance_sum(res, self.dm20))
res = prototype_selection_constructive_pMedian(self.dm20, 19)
self.assertCountEqual(
('A', 'B', 'C', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'D'),
res)
self.assertAlmostEqual(73.6075, distance_sum(res, self.dm20))
res = prototype_selection_constructive_pMedian(self.dm100, 5)
self.assertCountEqual(
('550.L1S167.s.1.sequence', '550.L1S117.s.1.sequence',
'550.L1S12.s.1.sequence', '550.L1S163.s.1.sequence',
'550.L1S148.s.1.sequence'),
res)
self.assertAlmostEqual(4.8783450, distance_sum(res, self.dm100))
res = prototype_selection_constructive_pMedian(self.dm100, 10)
self.assertCountEqual(
('550.L1S167.s.1.sequence', '550.L1S117.s.1.sequence',
'550.L1S12.s.1.sequence', '550.L1S163.s.1.sequence',
'550.L1S148.s.1.sequence', '550.L1S185.s.1.sequence',
'550.L1S133.s.1.sequence', '550.L1S126.s.1.sequence',
'550.L1S116.s.1.sequence', '550.L1S1.s.1.sequence'),
res)
self.assertAlmostEqual(23.75526307, distance_sum(res, self.dm100))
res = prototype_selection_constructive_pMedian(self.dm100, 20)
self.assertCountEqual(
('550.L1S167.s.1.sequence', '550.L1S117.s.1.sequence',
'550.L1S12.s.1.sequence', '550.L1S163.s.1.sequence',
'550.L1S148.s.1.sequence', '550.L1S185.s.1.sequence',
'550.L1S133.s.1.sequence', '550.L1S126.s.1.sequence',
'550.L1S116.s.1.sequence', '550.L1S1.s.1.sequence',
'550.L1S139.s.1.sequence', '550.L1S175.s.1.sequence',
'550.L1S176.s.1.sequence', '550.L1S181.s.1.sequence',
'550.L1S173.s.1.sequence', '550.L1S136.s.1.sequence',
'550.L1S16.s.1.sequence', '550.L1S123.s.1.sequence',
'550.L1S141.s.1.sequence', '550.L1S13.s.1.sequence'),
res)
self.assertAlmostEqual(100.32727028, distance_sum(res, self.dm100))
def test__protoclass(self):
res = _protoclass(self.dm20, 0.42)
self.assertCountEqual(('D', 'Q', 'A'), res)
self.assertAlmostEqual(1.7409, distance_sum(res, self.dm20))
res = _protoclass(self.dm20, 0.40)
self.assertCountEqual(('S', 'Q', 'A', 'B'), res)
self.assertAlmostEqual(3.1509, distance_sum(res, self.dm20))
res = _protoclass(self.dm20, 0.38)
self.assertCountEqual(('F', 'G', 'Q', 'A', 'B'), res)
self.assertAlmostEqual(5.1588, distance_sum(res, self.dm20))
res = _protoclass(self.dm20, 0.31)
self.assertCountEqual(
('D', 'I', 'A', 'B', 'C', 'E', 'F', 'G', 'J', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T'),
res)
self.assertAlmostEqual(66.4964, distance_sum(res, self.dm20))
res = _protoclass(self.dm20, 0.305)
self.assertCountEqual(
('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M',
'N', 'P', 'Q', 'R', 'S', 'T'),
res)
self.assertAlmostEqual(73.6075, distance_sum(res, self.dm20))
res = _protoclass(self.dm100, 0.5)
self.assertCountEqual(
('550.L1S1.s.1.sequence', '550.L1S105.s.1.sequence',
'550.L1S117.s.1.sequence', '550.L1S165.s.1.sequence',
'550.L1S167.s.1.sequence'),
res)
self.assertAlmostEqual(5.38708502529887, distance_sum(res, self.dm100))
res = _protoclass(self.dm100, 0.41)
self.assertCountEqual(
('550.L1S1.s.1.sequence', '550.L1S117.s.1.sequence',
'550.L1S133.s.1.sequence', '550.L1S136.s.1.sequence',
'550.L1S14.s.1.sequence', '550.L1S146.s.1.sequence',
'550.L1S149.s.1.sequence', '550.L1S163.s.1.sequence',
'550.L1S176.s.1.sequence', '550.L1S183.s.1.sequence'),
res)
self.assertAlmostEqual(25.0901634594939, distance_sum(res, self.dm100))
res = _protoclass(self.dm100, 0.374)
self.assertCountEqual(
('550.L1S1.s.1.sequence', '550.L1S103.s.1.sequence',
'550.L1S117.s.1.sequence', '550.L1S12.s.1.sequence',
'550.L1S127.s.1.sequence', '550.L1S128.s.1.sequence',
'550.L1S132.s.1.sequence', '550.L1S133.s.1.sequence',
'550.L1S136.s.1.sequence', '550.L1S139.s.1.sequence',
'550.L1S141.s.1.sequence', '550.L1S148.s.1.sequence',
'550.L1S16.s.1.sequence', '550.L1S163.s.1.sequence',
'550.L1S173.s.1.sequence', '550.L1S175.s.1.sequence',
'550.L1S176.s.1.sequence', '550.L1S18.s.1.sequence',
'550.L1S180.s.1.sequence', '550.L1S187.s.1.sequence'),
res)
self.assertAlmostEqual(101.91549799314, distance_sum(res, self.dm100))
# test seedset function, i.e. are 'A' and 'B' included in prototypes
res = _protoclass(self.dm20, 0.405, seedset=['A', 'B'])
self.assertCountEqual(res, ['A', 'B', 'D', 'Q'])
# test if at least one seed element is returned for too high epsilon
res = _protoclass(self.dm20, 0.805, seedset=['A', 'B'])
self.assertCountEqual(res, ['A', 'B'])
def test_prototype_selection_constructive_protoclass(self):
self.assertRaisesRegex(
RuntimeError,
"Number of iterations exceeded before",
prototype_selection_constructive_protoclass,
self.dm20,
5,
steps=1
)
self.assertRaisesRegex(
ValueError,
"must be >= 2, since a single",
prototype_selection_constructive_protoclass,
self.dm20,
1)
self.assertRaisesRegex(
ValueError,
"otherwise no reduction is necessary",
prototype_selection_constructive_protoclass,
self.dm20,
len(self.dm20.ids)+1)
res = prototype_selection_constructive_protoclass(self.dm20, 3)
self.assertCountEqual(('A', 'H', 'Q'), res)
self.assertAlmostEqual(1.7387, distance_sum(res, self.dm20))
res = prototype_selection_constructive_protoclass(self.dm20, 4)
self.assertCountEqual(('A', 'B', 'Q', 'G'), res)
self.assertAlmostEqual(3.278799999, distance_sum(res, self.dm20))
res = prototype_selection_constructive_protoclass(self.dm20, 5)
self.assertCountEqual(('H', 'C', 'G', 'Q', 'A'), res)
self.assertAlmostEqual(5.2747, distance_sum(res, self.dm20))
res = prototype_selection_constructive_protoclass(self.dm20, 18)
self.assertCountEqual(
('D', 'I', 'A', 'B', 'C', 'E', 'F', 'G', 'J', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T'),
res)
self.assertAlmostEqual(66.4964, distance_sum(res, self.dm20))
res = prototype_selection_constructive_protoclass(self.dm20, 19)
self.assertCountEqual(
('I', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'J', 'K', 'L', 'M',
'N', 'P', 'Q', 'R', 'S', 'T'),
res)
self.assertAlmostEqual(73.6075, distance_sum(res, self.dm20))
res = prototype_selection_constructive_protoclass(self.dm100, 5)
self.assertCountEqual(
('550.L1S156.s.1.sequence', '550.L1S105.s.1.sequence',
'550.L1S18.s.1.sequence', '550.L1S1.s.1.sequence',
'550.L1S165.s.1.sequence'),
res)
self.assertAlmostEqual(5.72452336845315, distance_sum(res, self.dm100))
res = prototype_selection_constructive_protoclass(self.dm100, 10)
self.assertCountEqual(
('550.L1S156.s.1.sequence', '550.L1S117.s.1.sequence',
'550.L1S14.s.1.sequence', '550.L1S182.s.1.sequence',
'550.L1S135.s.1.sequence', '550.L1S144.s.1.sequence',
'550.L1S1.s.1.sequence', '550.L1S146.s.1.sequence',
'550.L1S136.s.1.sequence', '550.L1S176.s.1.sequence'),
res)
self.assertAlmostEqual(24.9367079851425, distance_sum(res, self.dm100))
res = prototype_selection_constructive_protoclass(self.dm100, 20)
self.assertCountEqual(
('550.L1S163.s.1.sequence', '550.L1S117.s.1.sequence',
'550.L1S148.s.1.sequence', '550.L1S179.s.1.sequence',
'550.L1S128.s.1.sequence', '550.L1S12.s.1.sequence',
'550.L1S182.s.1.sequence', '550.L1S133.s.1.sequence',
'550.L1S127.s.1.sequence', '550.L1S139.s.1.sequence',
'550.L1S173.s.1.sequence', '550.L1S1.s.1.sequence',
'550.L1S141.s.1.sequence', '550.L1S165.s.1.sequence',
'550.L1S18.s.1.sequence', '550.L1S103.s.1.sequence',
'550.L1S16.s.1.sequence', '550.L1S136.s.1.sequence',
'550.L1S132.s.1.sequence', '550.L1S176.s.1.sequence'),
res)
self.assertAlmostEqual(101.104980832350, distance_sum(res, self.dm100))
def test_prototype_selection_destructive_maxdist(self):
self.assertRaisesRegex(
ValueError,
"must be >= 2, since a single",
prototype_selection_destructive_maxdist,
self.dm20,
1)
self.assertRaisesRegex(
ValueError,
"otherwise no reduction is necessary",
prototype_selection_destructive_maxdist,
self.dm20,
len(self.dm20.ids)+1)
res = prototype_selection_destructive_maxdist(self.dm20, 3)
self.assertCountEqual(('A', 'P', 'T'), res)
self.assertAlmostEqual(1.8389, distance_sum(res, self.dm20))
res = prototype_selection_destructive_maxdist(self.dm20, 4)
self.assertCountEqual(('A', 'P', 'T', 'C'), res)
self.assertAlmostEqual(3.4285, distance_sum(res, self.dm20))
res = prototype_selection_destructive_maxdist(self.dm20, 5)
self.assertCountEqual(('A', 'P', 'T', 'C', 'O'), res)
self.assertAlmostEqual(5.4494, distance_sum(res, self.dm20))
res = prototype_selection_destructive_maxdist(self.dm20, 18)
self.assertCountEqual(
('A', 'B', 'C', 'D', 'E', 'F', 'G', 'I', 'J', 'K', 'L', 'M', 'N',
'O', 'P', 'Q', 'R', 'T'),
res)
self.assertAlmostEqual(66.9400, distance_sum(res, self.dm20))
res = prototype_selection_destructive_maxdist(self.dm20, 19)
self.assertCountEqual(
('A', 'B', 'C', 'D', 'E', 'F', 'G', 'I', 'J', 'K', 'L', 'M', 'N',
'O', 'P', 'Q', 'R', 'T', 'S'),
res)
self.assertAlmostEqual(74.1234, distance_sum(res, self.dm20))
res = prototype_selection_destructive_maxdist(self.dm100, 5)
self.assertCountEqual(
('550.L1S1.s.1.sequence', '550.L1S13.s.1.sequence',
'550.L1S129.s.1.sequence', '550.L1S189.s.1.sequence',
'550.L1S176.s.1.sequence'),
res)
self.assertAlmostEqual(6.51661889263, distance_sum(res, self.dm100))
res = prototype_selection_destructive_maxdist(self.dm100, 10)
self.assertCountEqual(
('550.L1S1.s.1.sequence', '550.L1S147.s.1.sequence',
'550.L1S13.s.1.sequence', '550.L1S136.s.1.sequence',
'550.L1S15.s.1.sequence', '550.L1S115.s.1.sequence',
'550.L1S151.s.1.sequence', '550.L1S129.s.1.sequence',
'550.L1S189.s.1.sequence', '550.L1S176.s.1.sequence'),
res)
self.assertAlmostEqual(26.8818426729, distance_sum(res, self.dm100))
res = prototype_selection_destructive_maxdist(self.dm100, 20)
self.assertCountEqual(
('550.L1S1.s.1.sequence', '550.L1S173.s.1.sequence',
'550.L1S183.s.1.sequence', '550.L1S180.s.1.sequence',
'550.L1S135.s.1.sequence', '550.L1S18.s.1.sequence',
'550.L1S175.s.1.sequence', '550.L1S147.s.1.sequence',
'550.L1S134.s.1.sequence', '550.L1S13.s.1.sequence',
'550.L1S136.s.1.sequence', '550.L1S15.s.1.sequence',
'550.L1S132.s.1.sequence', '550.L1S115.s.1.sequence',
'550.L1S11.s.1.sequence', '550.L1S151.s.1.sequence',
'550.L1S121.s.1.sequence', '550.L1S129.s.1.sequence',
'550.L1S189.s.1.sequence', '550.L1S176.s.1.sequence'),
res)
self.assertAlmostEqual(106.991415187, distance_sum(res, self.dm100))