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test_res_alleles.py
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test_res_alleles.py
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"""
Copyright 2018 Kat Holt
Copyright 2018 Ryan Wick ([email protected])
https://github.com/katholt/Kleborate/
This file is part of Kleborate. Kleborate is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version. Kleborate is distributed in
the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along with Kleborate. If
not, see <http://www.gnu.org/licenses/>.
"""
import collections
import unittest
from kleborate.kleborate import get_output_headers, get_resistance_results
class TestResAlleles(unittest.TestCase):
"""
Tests calling of resistance via alleles.
"""
def setUp(self):
self.data_dir = 'test/res_test/data'
Args = collections.namedtuple('Args', ['resistance', 'kaptive_k', 'kaptive_o'])
self.args = Args(resistance=True, kaptive_k=False, kaptive_o=False)
_, _, self.res_headers = get_output_headers(self.args, self.data_dir)
def test_res_01(self):
results = get_resistance_results(self.data_dir, 'test/res_test/01.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertEqual(results['Bla'], 'ABC-1')
self.assertEqual(results['Bla_ESBL'], '-')
def test_res_02(self):
results = get_resistance_results(self.data_dir, 'test/res_test/02.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertEqual(results['Bla'], 'ABC-2')
self.assertEqual(results['Bla_ESBL'], '-')
def test_res_03(self):
results = get_resistance_results(self.data_dir, 'test/res_test/03.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertEqual(results['Bla'], '-')
self.assertEqual(results['Bla_ESBL'], 'ABC-3')
def test_res_04(self):
results = get_resistance_results(self.data_dir, 'test/res_test/04.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertEqual(results['Bla'], '-')
self.assertEqual(results['Bla_ESBL'], 'ABC-4')
def test_res_05(self):
results = get_resistance_results(self.data_dir, 'test/res_test/05.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertTrue(results['Bla'] == 'ABC-1^' or results['Bla'] == 'ABC-2^')
self.assertEqual(results['Bla_ESBL'], '-')
def test_res_06(self):
results = get_resistance_results(self.data_dir, 'test/res_test/06.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertEqual(results['Bla'], '-')
self.assertTrue(results['Bla_ESBL'] == 'ABC-3^' or results['Bla_ESBL'] == 'ABC-4^')
def test_res_07(self):
results = get_resistance_results(self.data_dir, 'test/res_test/07.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertEqual(results['Bla'], 'ABC-2*')
self.assertEqual(results['Bla_ESBL'], '-')
def test_res_08(self):
results = get_resistance_results(self.data_dir, 'test/res_test/08.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertEqual(results['Bla'], 'ABC-1;ABC-2')
self.assertEqual(results['Bla_ESBL'], '-')
def test_res_09(self):
results = get_resistance_results(self.data_dir, 'test/res_test/09.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertTrue(results['Bla'] == 'ABC-1^' or results['Bla'] == 'ABC-2^')
self.assertTrue(results['Bla_ESBL'] == 'ABC-3^' or results['Bla_ESBL'] == 'ABC-4^')
def test_res_10(self):
results = get_resistance_results(self.data_dir, 'test/res_test/10.fasta', self.args,
self.res_headers, True)
self.assertEqual(results['Tet'], '-')
self.assertEqual(results['Bla'], 'ABC-1;ABC-2')
self.assertEqual(results['Bla_ESBL'], 'ABC-3*;ABC-4')