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"""
Copyright 2020 Kat Holt
Copyright 2020 Ryan Wick (rrwick@gmail.com)
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.__main__ import get_data_path, get_output_headers, get_summary_results
class TestResScore(unittest.TestCase):
def setUp(self):
self.data_dir = get_data_path()
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)
self.results = {res_class: '-' for res_class in self.res_headers}
self.results['Yersiniabactin'] = '-'
self.results['Colibactin'] = '-'
self.results['Aerobactin'] = '-'
def test_nothing(self):
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '0')
self.assertEqual(summary_results['resistance_score'], '0')
self.assertEqual(summary_results['num_resistance_classes'], '0')
self.assertEqual(summary_results['num_resistance_genes'], '0')
def test_res_counts_1(self):
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b'
self.results['Tet_acquired'] = 'c'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '3')
def test_res_counts_2(self):
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b;c'
self.results['Tet_acquired'] = 'd;e;f'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '6')
def test_res_counts_3(self):
"""
Intrinsic Bla genes should not add to the counts.
"""
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b;c'
self.results['Tet_acquired'] = 'd;e;f'
self.results['Bla_acquired'] = 'g'
self.results['Bla_chr'] = 'h'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '4')
self.assertEqual(summary_results['num_resistance_genes'], '7')
def test_res_counts_4(self):
"""
Bla genes in columns other than 'Bla_chr' (e.g. 'Bla_ESBL_acquired') should add to the
counts.
"""
self.results['Tet_acquired'] = 'a;b;c'
self.results['Bla_chr'] = 'd'
self.results['Bla_ESBL_acquired'] = 'e'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '2')
self.assertEqual(summary_results['num_resistance_genes'], '4')
def test_res_counts_5(self):
"""
Bla genes in columns other than 'Bla_chr' (e.g. 'Bla_acquired') should add to the counts.
"""
self.results['Tet_acquired'] = 'a;b;c'
self.results['Bla_acquired'] = 'd'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '2')
self.assertEqual(summary_results['num_resistance_genes'], '4')
def test_res_counts_6(self):
"""
Omp gene truncations should not add to the gene or class counts.
"""
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b;c'
self.results['Tet_acquired'] = 'd;e;f'
self.results['Omp_mutations'] = 'g;h'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '6')
def test_res_counts_7(self):
"""
Mutations should add to the class count but not to the gene count (because that is for
acquired resistance genes).
"""
self.results['AGly_acquired'] = 'a'
self.results['Flq_mutations'] = 'b'
self.results['Tet_acquired'] = 'c;d;e'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '4')
def test_res_counts_8(self):
"""
Mutations should add to the class count but not to the gene count (because that is for
acquired resistance genes).
"""
self.results['AGly_acquired'] = 'a'
self.results['Flq_mutations'] = 'b;c'
self.results['Tet_acquired'] = 'd;e;f'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '4')
def test_res_counts_9(self):
"""
Mutations should add to the class count but not to the gene count (because that is for
acquired resistance genes).
"""
self.results['AGly_acquired'] = 'a'
self.results['Tet_acquired'] = 'b;c'
self.results['Col_mutations'] = 'd'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '3')
def test_res_counts_10(self):
"""
Resistance-by-truncation should add to the class count but not to the gene count (because
that is for acquired resistance genes).
"""
self.results['AGly_acquired'] = 'a'
self.results['Tet_acquired'] = 'b'
self.results['Col_acquired'] = 'c'
self.results['Col_mutations'] = 'd'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '3')
def test_res_counts_11(self):
"""
Spurious hits should not add to either the gene or class counts.
"""
self.results['AGly_acquired'] = 'a'
self.results['Flq_acquired'] = 'b'
self.results['Tet_acquired'] = 'c'
self.results['spurious_resistance_hits'] = 'd;e;f'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['num_resistance_classes'], '3')
self.assertEqual(summary_results['num_resistance_genes'], '3')
def test_res_score_1(self):
self.results['Bla_chr'] = 'a'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '0')
def test_res_score_2(self):
self.results['Bla_chr'] = 'a'
self.results['Bla_ESBL_acquired'] = 'b'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '1')
def test_res_score_3(self):
self.results['Bla_chr'] = 'a'
self.results['Bla_ESBL_inhR_acquired'] = 'b'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '1')
def test_res_score_4(self):
self.results['Bla_chr'] = 'a'
self.results['Bla_Carb_acquired'] = 'b'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '2')
def test_res_score_5(self):
self.results['Bla_chr'] = 'a'
self.results['Bla_ESBL_acquired'] = 'b'
self.results['Bla_Carb_acquired'] = 'c'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '2')
def test_res_score_6(self):
self.results['Bla_chr'] = 'a'
self.results['Bla_ESBL_acquired'] = 'b'
self.results['Bla_Carb_acquired'] = 'c'
self.results['Col_acquired'] = 'd'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '3')
def test_res_score_7(self):
self.results['Bla_chr'] = 'a'
self.results['Bla_ESBL_acquired'] = 'b'
self.results['Bla_Carb_acquired'] = 'c'
self.results['Col_mutations'] = 'd'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '3')
def test_res_score_8(self):
self.results['Col_acquired'] = 'a'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['resistance_score'], '0')
def test_vir_score_1(self):
self.results['Yersiniabactin'] = 'a'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '1')
def test_vir_score_2(self):
self.results['Colibactin'] = 'a'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '2')
def test_vir_score_3(self):
self.results['Colibactin'] = 'a'
self.results['Yersiniabactin'] = 'b'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '2')
def test_vir_score_4(self):
self.results['Aerobactin'] = 'a'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '3')
def test_vir_score_5(self):
self.results['Aerobactin'] = 'a'
self.results['Yersiniabactin'] = 'b'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '4')
def test_vir_score_6(self):
self.results['Aerobactin'] = 'a'
self.results['Colibactin'] = 'b'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '5')
def test_vir_score_7(self):
self.results['Aerobactin'] = 'a'
self.results['Colibactin'] = 'b'
self.results['Yersiniabactin'] = 'c'
summary_results = get_summary_results(self.results, self.res_headers, self.args)
self.assertEqual(summary_results['virulence_score'], '5')
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