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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.
# ----------------------------------------------------------------------------
import glob
import unittest
import tempfile
import os.path
import biom
import numpy as np
import pandas as pd
import pandas.testing as pdt
from q2_feature_table import core_features
from q2_feature_table._core_features._visualizer import (
_get_core_features, _seven_number_summary, _round_fractions)
class TestCoreFeatures(unittest.TestCase):
def setUp(self):
self.table = biom.Table(np.array([[0, 11, 11], [13, 11, 11]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
self.output_dir_obj = tempfile.TemporaryDirectory(
prefix='q2-feature-table-test-temp-')
self.output_dir = self.output_dir_obj.name
def tearDown(self):
self.output_dir_obj.cleanup()
def assertBasicVizValidity(self, viz_dir, exp_sample_count=3,
exp_feature_count=2, exp_no_core=False,
exp_no_plot=False):
index_fp = os.path.join(viz_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp, 'r') as fh:
index_contents = fh.read()
self.assertIn('Sample count: %d' % exp_sample_count, index_contents)
self.assertIn('Feature count: %d' % exp_feature_count, index_contents)
if exp_no_core:
self.assertIn('No core features', index_contents)
if exp_no_plot:
self.assertIn('only one data point', index_contents)
else:
svg_fp = os.path.join(viz_dir, 'core-feature-counts.svg')
self.assertTrue(os.path.exists(svg_fp))
def assertCoreFeaturesPresent(self, filepath, positive_ids, negative_ids):
self.assertTrue(os.path.exists(filepath))
with open(filepath, 'r') as fh:
contents = fh.read()
for positive_id in positive_ids:
self.assertIn(positive_id, contents)
for negative_id in negative_ids:
self.assertNotIn(negative_id, contents)
def test_defaults(self):
core_features(self.output_dir, self.table)
self.assertBasicVizValidity(self.output_dir)
core_50_fp = os.path.join(self.output_dir, 'core-features-0.500.tsv')
self.assertCoreFeaturesPresent(core_50_fp, ['O1', 'O2'], [])
core_100_fp = os.path.join(self.output_dir, 'core-features-1.000.tsv')
self.assertCoreFeaturesPresent(core_100_fp, ['O2'], ['O1'])
def test_fraction_range(self):
core_features(self.output_dir, self.table, min_fraction=0.55,
max_fraction=0.95, steps=9)
self.assertBasicVizValidity(self.output_dir)
core_50_fp = os.path.join(self.output_dir, 'core-features-0.500.tsv')
self.assertFalse(os.path.exists(core_50_fp))
core_55_fp = os.path.join(self.output_dir, 'core-features-0.550.tsv')
self.assertCoreFeaturesPresent(core_55_fp, ['O1', 'O2'], [])
core_95_fp = os.path.join(self.output_dir, 'core-features-0.950.tsv')
self.assertCoreFeaturesPresent(core_95_fp, ['O2'], ['O1'])
core_100_fp = os.path.join(self.output_dir, 'core-features-1.000.tsv')
self.assertFalse(os.path.exists(core_100_fp))
def test_minimum_number_of_steps(self):
core_features(self.output_dir, self.table, min_fraction=0.55,
max_fraction=0.95, steps=2)
self.assertBasicVizValidity(self.output_dir)
core_55_fp = os.path.join(self.output_dir, 'core-features-0.550.tsv')
core_95_fp = os.path.join(self.output_dir, 'core-features-0.950.tsv')
tsv_files = sorted(glob.glob(os.path.join(self.output_dir, '*.tsv')))
self.assertEqual(tsv_files, [core_55_fp, core_95_fp])
self.assertCoreFeaturesPresent(core_55_fp, ['O1', 'O2'], [])
self.assertCoreFeaturesPresent(core_95_fp, ['O2'], ['O1'])
def test_equal_min_max_fractions(self):
core_features(self.output_dir, self.table, min_fraction=0.55,
max_fraction=0.55)
self.assertBasicVizValidity(self.output_dir, exp_no_plot=True)
core_55_fp = os.path.join(self.output_dir, 'core-features-0.550.tsv')
tsv_files = glob.glob(os.path.join(self.output_dir, '*.tsv'))
self.assertEqual(tsv_files, [core_55_fp])
self.assertCoreFeaturesPresent(core_55_fp, ['O1', 'O2'], [])
def test_tiny_steps_precision(self):
# Bug in a previous iteration of the code used a fixed number of digits
# in the "feature list" TSV filenames, causing files to be overwritten
# with the wrong data if a small enough step size was used.
core_features(self.output_dir, self.table, min_fraction=0.1,
max_fraction=0.11, steps=101)
self.assertBasicVizValidity(self.output_dir)
fp = os.path.join(self.output_dir, 'core-features-0.1000.tsv')
self.assertTrue(os.path.exists(fp))
fp = os.path.join(self.output_dir, 'core-features-0.1001.tsv')
self.assertTrue(os.path.exists(fp))
fp = os.path.join(self.output_dir, 'core-features-0.1099.tsv')
self.assertTrue(os.path.exists(fp))
fp = os.path.join(self.output_dir, 'core-features-0.1100.tsv')
self.assertTrue(os.path.exists(fp))
def test_no_core_features(self):
table = biom.Table(np.array([[0, 11, 11], [11, 11, 0]]), ['O1', 'O2'],
['S1', 'S2', 'S3'])
core_features(self.output_dir, table)
self.assertBasicVizValidity(self.output_dir, exp_no_core=True)
core_50_fp = os.path.join(self.output_dir, 'core-features-0.500.tsv')
self.assertCoreFeaturesPresent(core_50_fp, ['O1', 'O2'], [])
# No core features exist at fraction=1.0
core_100_fp = os.path.join(self.output_dir, 'core-features-1.000.tsv')
self.assertFalse(os.path.exists(core_100_fp))
def test_empty_table(self):
table = biom.Table(np.array([[]]), [], [])
core_features(self.output_dir, table)
self.assertBasicVizValidity(self.output_dir, exp_sample_count=0,
exp_feature_count=0, exp_no_core=True)
self.assertFalse(glob.glob(os.path.join(self.output_dir, '*.tsv')))
def test_invalid_parameters(self):
with self.assertRaisesRegex(ValueError, 'fraction'):
core_features(self.output_dir, self.table, min_fraction=0.75,
max_fraction=0.5)
class TestCoreFeaturesPrivateFunctions(unittest.TestCase):
# Most of the work happens in private functions for this visualizer,
# so it's important to have some tests of the private functionality
def test_seven_number_summary(self):
# validated against calling pd.Series.describe directly
exp = pd.Series([11., 11., 11., 11., 12., 12.64, 12.92],
index=['2%', '9%', '25%', '50%', '75%', '91%', '98%'])
pdt.assert_series_equal(_seven_number_summary([13, 11, 11]), exp)
exp = pd.Series([1., 1., 1., 1., 1., 1., 1.],
index=['2%', '9%', '25%', '50%', '75%', '91%', '98%'])
pdt.assert_series_equal(_seven_number_summary([1]), exp)
exp = pd.Series([np.nan, np.nan, np.nan, np.nan, np.nan,
np.nan, np.nan],
index=['2%', '9%', '25%', '50%', '75%', '91%', '98%'])
pdt.assert_series_equal(_seven_number_summary([]), exp)
def test_get_core_features(self):
table = biom.Table(np.array([[0, 11, 11], [13, 11, 11]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
o2_seven_num = pd.Series(
[11., 11., 11., 11., 12., 12.64, 12.92],
index=['2%', '9%', '25%', '50%', '75%', '91%', '98%'])
exp = pd.DataFrame([o2_seven_num], index=['O2'])
obs = _get_core_features(table, fraction=0.67)
pdt.assert_frame_equal(obs, exp)
obs = _get_core_features(table, fraction=1.0)
pdt.assert_frame_equal(obs, exp)
def test_get_core_features_all(self):
table = biom.Table(np.array([[0, 11, 11], [13, 11, 11]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
o1_seven_num = pd.Series(
[0.44, 1.98, 5.5, 11., 11., 11., 11.],
index=['2%', '9%', '25%', '50%', '75%', '91%', '98%'])
o2_seven_num = pd.Series(
[11., 11., 11., 11., 12., 12.64, 12.92],
index=['2%', '9%', '25%', '50%', '75%', '91%', '98%'])
exp = pd.DataFrame([o1_seven_num, o2_seven_num], index=['O1', 'O2'])
# fraction = 2/3 - 0.006
obs = _get_core_features(table, fraction=0.660)
pdt.assert_frame_equal(obs, exp)
obs = _get_core_features(table, fraction=0.0)
pdt.assert_frame_equal(obs, exp)
def test_round_fractions_single(self):
obs = _round_fractions([0.0])
self.assertEqual(obs, ['0.000'])
obs = _round_fractions([0.1236])
self.assertEqual(obs, ['0.124'])
def test_round_fractions_3_decimals(self):
obs = _round_fractions([0.1236, 0.45, 0.123])
self.assertEqual(obs, ['0.124', '0.450', '0.123'])
def test_round_fractions_4_decimals(self):
obs = _round_fractions([0.1234, 0.45, 0.0, 0.12346])
self.assertEqual(obs, ['0.1234', '0.4500', '0.0000', '0.1235'])
def test_round_fractions_full_precision(self):
obs = _round_fractions([0.01234567890, 0.01234567891])
self.assertEqual(obs, ['0.0123456789', '0.01234567891'])
if __name__ == "__main__":
unittest.main()
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