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# ----------------------------------------------------------------------------
# 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 rarefy
class RarefyTests(TestCase):
def test_rarefy(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
a = rarefy(t, 2)
self.assertEqual(a.shape, (2, 2))
self.assertEqual(set(a.ids(axis='sample')), set(['S2', 'S3']))
self.assertEqual(set(a.ids(axis='observation')), set(['O1', 'O2']))
npt.assert_array_equal(a.sum(axis='sample'), np.array([2., 2.]))
def test_rarefy_replacement(self):
t = Table(np.array([[0, 10, 30], [10, 10, 20]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
rt = rarefy(t, 3, with_replacement=True)
self.assertEqual(rt.shape, (2, 3))
# IMPORTANT: samples below subsample depth should be removed
for n_draws in range(11, 21):
rt = rarefy(t, n_draws, with_replacement=True)
npt.assert_array_equal(rt.sum('sample'),
np.array([n_draws] * 2))
for n_draws in range(21, 50):
rt = rarefy(t, n_draws, with_replacement=True)
npt.assert_array_equal(rt.sum('sample'),
np.array([n_draws] * 1))
def test_rarefy_depth_error(self):
t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, 'shallow enough'):
rarefy(t, 50)
if __name__ == "__main__":
main()
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