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
|
# ----------------------------------------------------------------------------
# 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 relative_frequency, presence_absence, transpose
class RelativeFrequencyTests(TestCase):
def test_relative_frequency(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
a = relative_frequency(t)
self.assertEqual(a.shape, (2, 3))
self.assertEqual(set(a.ids(axis='sample')), set(['S1', 'S2', 'S3']))
self.assertEqual(set(a.ids(axis='observation')), set(['O1', 'O2']))
npt.assert_array_equal(a.sum(axis='sample'), np.array([1., 1., 1.]))
npt.assert_array_equal(a.matrix_data.toarray(),
np.array([[0, 0.5, 3/5], [1.0, 0.5, 2/5]]))
class PresenceAbsenceTests(TestCase):
def test_presence_absence(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
a = presence_absence(t)
self.assertEqual(a.shape, (2, 3))
self.assertEqual(set(a.ids(axis='sample')), set(['S1', 'S2', 'S3']))
self.assertEqual(set(a.ids(axis='observation')), set(['O1', 'O2']))
npt.assert_array_equal(a.matrix_data.toarray(),
np.array([[0, 1, 1], [1, 1, 1]]))
class TransposeTests(TestCase):
def test_transpose(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
a = transpose(t)
self.assertEqual(a.shape, (3, 2))
self.assertEqual(set(a.ids(axis='sample')), set(['O1', 'O2']))
self.assertEqual(set(a.ids(axis='observation')),
set(['S1', 'S2', 'S3']))
if __name__ == "__main__":
main()
|
