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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_rmp_mlst_results, get_rmpa2_results
class TestRmp(unittest.TestCase):
"""
Tests RmpADC ST calls.
"""
def setUp(self):
self.data_dir = 'test/test_rmp/data'
Args = collections.namedtuple('Args', ['min_coverage', 'min_identity',
'min_spurious_coverage', 'min_spurious_identity'])
self.args = Args(min_coverage=80.0, min_identity=90.0,
min_spurious_coverage=40.0, min_spurious_identity=80.0)
def test_rmp_random(self):
"""
This test has just random sequence and should give no rmp call.
"""
results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_random.fasta', self.args)
self.assertEqual(results['rmpA'], '-')
self.assertEqual(results['rmpD'], '-')
self.assertEqual(results['rmpC'], '-')
self.assertEqual(results['RmpADC'], '-')
self.assertEqual(results['RmST'], '0')
def test_rmp_19(self):
"""
This test is an exact match for RmST19, an ST without any truncated alleles.
"""
results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_rmp_1.fasta', self.args)
self.assertEqual(results['rmpA'], '7')
self.assertEqual(results['rmpD'], '8')
self.assertEqual(results['rmpC'], '3')
self.assertEqual(results['RmpADC'], 'rmp 2A; VP')
self.assertEqual(results['RmST'], '19')
def test_rmp_21(self):
"""
This test is an exact match for RmST21, an ST with a truncated allele.
"""
results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_rmp_2.fasta', self.args)
self.assertEqual(results['rmpA'], '7')
self.assertEqual(results['rmpD'], '36')
self.assertEqual(results['rmpC'], '4-17%')
self.assertEqual(results['RmpADC'], 'rmp 2A; VP (truncated)')
self.assertEqual(results['RmST'], '21')
def test_rmp_novel(self):
"""
This test is an exact match for alleles, but an unknown combination.
"""
results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_rmp_3.fasta', self.args)
self.assertEqual(results['rmpA'], '8')
self.assertEqual(results['rmpD'], '1')
self.assertEqual(results['rmpC'], '9-11%')
self.assertEqual(results['RmpADC'], 'rmp unknown')
self.assertEqual(results['RmST'], '0')
def test_rmp_missing_1(self):
"""
This test is a match for RmST1, except that it's missing rmpC.
"""
results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_rmp_4.fasta', self.args)
self.assertEqual(results['rmpA'], '41-54%')
self.assertEqual(results['rmpD'], '20')
self.assertEqual(results['rmpC'], '-')
self.assertEqual(results['RmpADC'], 'rmp 2A; VP (incomplete) (truncated)')
self.assertEqual(results['RmST'], '1-1LV')
def test_rmpa2_random(self):
"""
This test has just random sequence and should give no rmpA2 call.
"""
results = get_rmpa2_results(self.data_dir, 'test/test_rmp/test_random.fasta', self.args)
self.assertEqual(results['rmpA2'], '-')
def test_rmpa2_exact(self):
"""
This test has an exact match for rmpA2_1.
"""
results = get_rmpa2_results(self.data_dir, 'test/test_rmp/test_rmpa2_1.fasta', self.args)
self.assertEqual(results['rmpA2'], 'rmpA2_1')
def test_rmpa2_exact_truncated(self):
"""
This test has an exact match for rmpA2_7.
"""
results = get_rmpa2_results(self.data_dir, 'test/test_rmp/test_rmpa2_2.fasta', self.args)
self.assertEqual(results['rmpA2'], 'rmpA2_7-47%')
def test_rmpa2_inexact(self):
"""
This test has an inexact match for rmpA2_1.
"""
results = get_rmpa2_results(self.data_dir, 'test/test_rmp/test_rmpa2_3.fasta', self.args)
self.assertEqual(results['rmpA2'], 'rmpA2_1*')
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