1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
|
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from unittest import TestCase, main
import numpy as np
import numpy.testing as npt
from biom.table import Table
from q2_feature_table import subsample
class SubsampleTests(TestCase):
def test_subsample_samples(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
a = subsample(t, 2, 'sample')
self.assertEqual(a.shape, (2, 2))
sample_ids = frozenset(a.ids(axis='sample'))
self.assertIn(sample_ids, set([frozenset(['S1', 'S2']),
frozenset(['S1', 'S3']),
frozenset(['S2', 'S3'])]))
self.assertEqual(set(a.ids(axis='observation')), set(['O1', 'O2']))
for i in a.ids(axis='sample'):
npt.assert_equal(t.data(i, axis='sample'),
a.data(i, axis='sample'))
def test_subsample_features(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]).T,
['O1', 'O2', 'O3'],
['S1', 'S2'])
a = subsample(t, 2, 'feature')
self.assertEqual(a.shape, (2, 2))
sample_ids = frozenset(a.ids(axis='observation'))
self.assertIn(sample_ids, set([frozenset(['O1', 'O2']),
frozenset(['O1', 'O3']),
frozenset(['O2', 'O3'])]))
self.assertEqual(set(a.ids(axis='sample')), set(['S1', 'S2']))
for i in a.ids(axis='observation'):
npt.assert_equal(t.data(i, axis='observation'),
a.data(i, axis='observation'))
def test_subsample_samples_oversample(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]).T,
['O1', 'O2', 'O3'],
['S1', 'S2'])
with self.assertRaisesRegex(ValueError, "depth exceeds"):
subsample(t, 10, 'sample')
def test_subsample_features_oversample(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]).T,
['O1', 'O2', 'O3'],
['S1', 'S2'])
with self.assertRaisesRegex(ValueError, "depth exceeds"):
subsample(t, 10, 'feature')
def test_subsample_samples_empty(self):
t = Table(np.array([[0, 0, 0], [0, 0, 0]]).T,
['O1', 'O2', 'O3'],
['S1', 'S2'])
with self.assertRaisesRegex(ValueError, "contains no"):
subsample(t, 2, 'sample')
def test_subsample_features_empty(self):
t = Table(np.array([[0, 0, 0], [0, 0, 0]]).T,
['O1', 'O2', 'O3'],
['S1', 'S2'])
with self.assertRaisesRegex(ValueError, "contains no"):
subsample(t, 2, 'feature')
if __name__ == "__main__":
main()
|
