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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 tempfile
import os
import unittest
from kleborate.__main__ import get_output_headers, get_strain_name, get_contig_stat_results, \
get_species_results, is_kp_complex, get_chromosome_mlst_results, get_ybt_mlst_results, \
get_clb_mlst_results, get_iuc_mlst_results, get_iro_mlst_results, get_rmp_mlst_results,\
get_rmpa2_results, get_wzi_and_k_locus_results, get_resistance_results, get_summary_results, \
gunzip_contigs_if_necessary
def load_result_headers():
with open('test/test_genomes/test_genome_results.txt', 'rt') as results:
for line in results:
parts = line.strip('\n').split('\t')
assert parts[0] == 'strain'
return parts
def load_results_one_genome(genome_name):
with open('test/test_genomes/test_genome_results.txt', 'rt') as results:
for line in results:
parts = line.strip('\n').split('\t')
if parts[0] == genome_name:
return parts
assert False
def load_correct_results(filename):
genome_name = os.path.basename(filename)
genome_name = genome_name.replace('.fasta.gz', '').replace('.fna.gz', '')
headers = load_result_headers()
results = load_results_one_genome(genome_name)
assert len(headers) == len(results)
return dict(zip(headers, results))
class TestGenomes(unittest.TestCase):
def setUp(self):
self.data_dir = 'test/test_genomes/data'
Args = collections.namedtuple('Args', ['resistance', 'kaptive_k', 'kaptive_o',
'min_coverage', 'min_identity'])
self.args = Args(resistance=True, kaptive_k=False, kaptive_o=False,
min_coverage=80.0, min_identity=90.0)
_, _, self.res_headers = get_output_headers(self.args, self.data_dir)
def one_genome_test(self, filename):
correct_results = load_correct_results(filename)
with tempfile.TemporaryDirectory() as tmp_dir:
contigs = gunzip_contigs_if_necessary(filename, tmp_dir)
test_results = self.get_all_results(contigs)
for result, value in correct_results.items():
if value != '':
assert test_results[result] == value
def get_all_results(self, contigs):
results = {'strain': get_strain_name(contigs)}
results.update(get_species_results(contigs, self.data_dir))
kp_complex = is_kp_complex(results)
results.update(get_contig_stat_results(contigs, is_kp_complex))
results.update(get_chromosome_mlst_results(self.data_dir, contigs, kp_complex, self.args))
results.update(get_ybt_mlst_results(self.data_dir, contigs, self.args))
results.update(get_clb_mlst_results(self.data_dir, contigs, self.args))
results.update(get_iuc_mlst_results(self.data_dir, contigs, self.args))
results.update(get_iro_mlst_results(self.data_dir, contigs, self.args))
results.update(get_rmp_mlst_results(self.data_dir, contigs, self.args))
results.update(get_rmpa2_results(self.data_dir, contigs, self.args))
results.update(get_wzi_and_k_locus_results(self.data_dir, contigs, self.args))
results.update(get_resistance_results(self.data_dir, contigs, self.args, self.res_headers,
kp_complex))
results.update(get_summary_results(results, self.res_headers))
return results
def test_172(self):
self.one_genome_test('test/test_genomes/172.fasta.gz')
def test_24042_7_219(self):
self.one_genome_test('test/test_genomes/24042_7#219.fasta.gz')
def test_24042_7_351(self):
self.one_genome_test('test/test_genomes/24042_7#351.fasta.gz')
def test_2685(self):
self.one_genome_test('test/test_genomes/2685.fasta.gz')
def test_AS7(self):
self.one_genome_test('test/test_genomes/AS7.fna.gz')
def test_BA4471(self):
self.one_genome_test('test/test_genomes/BA4471.fasta.gz')
def test_BA7971(self):
self.one_genome_test('test/test_genomes/BA7971.fasta.gz')
def test_CM3425(self):
self.one_genome_test('test/test_genomes/CM3425.fasta.gz')
def test_ERR2835900(self):
self.one_genome_test('test/test_genomes/ERR2835900.fna.gz')
def test_GCA_901563875(self):
self.one_genome_test('test/test_genomes/GCA_901563875.1.fna.gz')
def test_GCA_902158585(self):
self.one_genome_test('test/test_genomes/GCA_902158585.1.fna.gz')
def test_GCF_000009885(self):
self.one_genome_test('test/test_genomes/GCF_000009885.1.fna.gz')
def test_GCF_000016305(self):
self.one_genome_test('test/test_genomes/GCF_000016305.1.fna.gz')
def test_GCF_000019565(self):
self.one_genome_test('test/test_genomes/GCF_000019565.1.fna.gz')
def test_GCF_000215745(self):
self.one_genome_test('test/test_genomes/GCF_000215745.1.fna.gz')
def test_GCF_000240325(self):
self.one_genome_test('test/test_genomes/GCF_000240325.1.fna.gz')
def test_GCF_000247855(self):
self.one_genome_test('test/test_genomes/GCF_000247855.1.fna.gz')
def test_GCF_000247895(self):
self.one_genome_test('test/test_genomes/GCF_000247895.1.fna.gz')
def test_GCF_000492415(self):
self.one_genome_test('test/test_genomes/GCF_000492415.1.fna.gz')
def test_GCF_000492795(self):
self.one_genome_test('test/test_genomes/GCF_000492795.1.fna.gz')
def test_GCF_000523395(self):
self.one_genome_test('test/test_genomes/GCF_000523395.1.fna.gz')
def test_GCF_000648315(self):
self.one_genome_test('test/test_genomes/GCF_000648315.1.fna.gz')
def test_GCF_000733495(self):
self.one_genome_test('test/test_genomes/GCF_000733495.1.fna.gz')
def test_GCF_000829965(self):
self.one_genome_test('test/test_genomes/GCF_000829965.1.fna.gz')
def test_GCF_000968155(self):
self.one_genome_test('test/test_genomes/GCF_000968155.1.fna.gz')
def test_GCF_001068035(self):
self.one_genome_test('test/test_genomes/GCF_001068035.1.fna.gz')
def test_GCF_002108345(self):
self.one_genome_test('test/test_genomes/GCF_002108345.1.fna.gz')
def test_GCF_002247645(self):
self.one_genome_test('test/test_genomes/GCF_002247645.1.fna.gz')
def test_GCF_002248955(self):
self.one_genome_test('test/test_genomes/GCF_002248955.1.fna.gz')
def test_GCF_002806645(self):
self.one_genome_test('test/test_genomes/GCF_002806645.1.fna.gz')
def test_GCF_003095495(self):
self.one_genome_test('test/test_genomes/GCF_003095495.1.fna.gz')
def test_GCF_003345475(self):
self.one_genome_test('test/test_genomes/GCF_003345475.1.fna.gz')
def test_GCF_003400925(self):
self.one_genome_test('test/test_genomes/GCF_003400925.1.fna.gz')
def test_GCF_003937345(self):
self.one_genome_test('test/test_genomes/GCF_003937345.1.fna.gz')
def test_GCF_004010735(self):
self.one_genome_test('test/test_genomes/GCF_004010735.1.fna.gz')
def test_GCF_005860775(self):
self.one_genome_test('test/test_genomes/GCF_005860775.1.fna.gz')
def test_GCF_900501255(self):
self.one_genome_test('test/test_genomes/GCF_900501255.1.fna.gz')
# def test_GCF_900501255(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_900501255.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '0')
# self.assertEqual(results['rmpA'], 'rmpA_2(KpVP-1)')
# self.assertEqual(results['rmpA2'], 'rmpA2_4*-50%')
# self.assertEqual(results['AGly'], '-')
# self.assertEqual(results['Col'], '-')
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], '-')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], '-')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], '-')
# self.assertEqual(results['Tet'], '-')
# self.assertEqual(results['Tmt'], '-')
# self.assertEqual(results['Omp'], '-')
# self.assertEqual(results['Bla'], 'SHV-187*')
# self.assertEqual(results['Bla_Carb'], '-')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], '-')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_GCF_003400925(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_003400925.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '5')
# self.assertEqual(results['rmpA'], '-')
# self.assertEqual(results['rmpA2'], 'rmpA2_9')
# self.assertEqual(results['AGly'], 'RmtC')
# self.assertEqual(results['Col'], '-')
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], 'GyrA-83I;ParC-80I')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], '-')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], 'SulI')
# self.assertEqual(results['Tet'], 'TetA')
# self.assertEqual(results['Tmt'], 'DfrA1')
# self.assertEqual(results['Omp'], '-')
# self.assertEqual(results['Bla'], '-')
# self.assertEqual(results['Bla_Carb'], 'NDM-1')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], 'SHV-11')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_GCF_001068035(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_001068035.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '0')
# self.assertEqual(results['rmpA'], 'rmpA_2(KpVP-1)')
# self.assertEqual(results['rmpA2'], 'rmpA2_3*-0%')
# self.assertEqual(results['AGly'], '-')
#
# # PmrB is split in two: 40% (start) and 60% (end). The correct answer is 40% as that
# # includes the beginning of the gene.
# self.assertEqual(results['Col'], 'PmrB-40%')
#
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], '-')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], '-')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], '-')
# self.assertEqual(results['Tet'], '-')
# self.assertEqual(results['Tmt'], '-')
# self.assertEqual(results['Omp'], '-')
# self.assertEqual(results['Bla'], '-')
# self.assertEqual(results['Bla_Carb'], '-')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], '-')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_GCF_003095495(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_003095495.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '17')
# self.assertEqual(results['rmpA'], '-')
# self.assertEqual(results['rmpA2'], '-')
# self.assertEqual(results['AGly'], 'Aac3-IId^;AadA2^;Aph3-Ia^;RmtB;Sat-2A;StrA^;StrB')
#
# # PmrB is split in two: 36% (start) and 66% (end). The correct answer is 36% as that
# # includes the beginning of the gene.
# self.assertEqual(results['Col'], 'MgrB-62%;PmrB-36%')
#
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], 'GyrA-83I;ParC-80I')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], 'Erm42*;MphA')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], 'CatA1^')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], 'SulI;SulII')
# self.assertEqual(results['Tet'], 'TetG')
# self.assertEqual(results['Tmt'], 'DfrA12?')
# self.assertEqual(results['Omp'], 'OmpK35-25%;OmpK36GD')
# self.assertEqual(results['Bla'], 'TEM-1D^')
# self.assertEqual(results['Bla_Carb'], 'KPC-2')
# self.assertEqual(results['Bla_ESBL'], 'CTX-M-14')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], 'SHV-11')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_GCF_000009885(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_000009885.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '0')
# self.assertEqual(results['rmpA'], 'rmpA_11(ICEKp1),rmpA_2(KpVP-1)')
# self.assertEqual(results['rmpA2'], 'rmpA2_3-47%')
# self.assertEqual(results['AGly'], '-')
# self.assertEqual(results['Col'], '-')
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], '-')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], '-')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], '-')
# self.assertEqual(results['Tet'], '-')
# self.assertEqual(results['Tmt'], '-')
# self.assertEqual(results['Omp'], '-')
# self.assertEqual(results['Bla'], '-')
# self.assertEqual(results['Bla_Carb'], '-')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], 'SHV-11^')
# self.assertEqual(results['Bla_broad_inhR'], '-')
# self.assertEqual(results['wzi'], 'wzi1')
# self.assertEqual(results['K_locus'], 'KL1')
#
# def test_GCF_004010735(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_004010735.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['wzi'], '-')
# self.assertEqual(results['K_locus'], '-')
#
# def test_GCF_000968155(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_000968155.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '0')
# self.assertEqual(results['rmpA'], 'rmpA_9(KpVP-2)')
# self.assertEqual(results['rmpA2'], '-')
# self.assertEqual(results['AGly'], '-')
# self.assertEqual(results['Col'], '-')
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], '-')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], '-')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], '-')
# self.assertEqual(results['Tet'], '-')
# self.assertEqual(results['Tmt'], '-')
# self.assertEqual(results['Omp'], '-')
# self.assertEqual(results['Bla'], '-')
# self.assertEqual(results['Bla_Carb'], '-')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], '-')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_GCF_002108345(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_002108345.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '11')
# self.assertEqual(results['rmpA'], '-')
# self.assertEqual(results['rmpA2'], '-')
# self.assertEqual(results['AGly'], 'Aac3-IId^;Aph3-Ia^')
# self.assertEqual(results['Col'], '-')
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], 'GyrA-83I;ParC-80I;QnrB4;QnrB4')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], 'CatA2*;CatB3*')
# self.assertEqual(results['Rif'], 'Arr3')
# self.assertEqual(results['Sul'], 'SulI*;SulI^')
# self.assertEqual(results['Tet'], '-')
# self.assertEqual(results['Tmt'], '-')
# self.assertEqual(results['Omp'], 'OmpK35-18%')
# self.assertEqual(results['Bla'], 'DHA-1;OXA-1;SHV-187*')
# self.assertEqual(results['Bla_Carb'], '-')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], '-')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_GCF_002247645(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_002247645.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '7')
# self.assertEqual(results['rmpA'], '-')
# self.assertEqual(results['rmpA2'], '-')
# self.assertEqual(results['AGly'], 'Aac3-IId^')
# self.assertEqual(results['Col'], '-')
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], 'Qnr-S1')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], 'FloR*')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], '-')
# self.assertEqual(results['Tet'], 'TetA*')
# self.assertEqual(results['Tgc'], 'TetX4')
# self.assertEqual(results['Tmt'], '-')
# self.assertEqual(results['Omp'], '-')
# self.assertEqual(results['Bla'], 'LAP-2;SHV-2a^;TEM-1D^')
# self.assertEqual(results['Bla_Carb'], '-')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], '-')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_GCF_002248955(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_002248955.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '4')
# self.assertEqual(results['rmpA'], '-')
# self.assertEqual(results['rmpA2'], '-')
# self.assertEqual(results['AGly'], 'Aac3-IId^')
# self.assertEqual(results['Col'], 'Mcr3-1*')
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], 'GyrA-83F;GyrA-87A;ParC-80I')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], 'CatA1^')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], '-')
# self.assertEqual(results['Tet'], 'TetA')
# self.assertEqual(results['Tmt'], '-')
# self.assertEqual(results['Omp'], '-')
# self.assertEqual(results['Bla'], 'SHV-28^')
# self.assertEqual(results['Bla_Carb'], '-')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], '-')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_GCF_003345475(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/GCF_003345475.1.fna.gz',
# tmp_dir)
# results = self.get_all_results(contigs)
# self.assertEqual(results['num_resistance_genes'], '5')
# self.assertEqual(results['rmpA'], '-')
# self.assertEqual(results['rmpA2'], '-')
# self.assertEqual(results['AGly'], '-')
# self.assertEqual(results['Col'], 'Mcr1-1;MgrB-49%')
# self.assertEqual(results['Fcyn'], '-')
# self.assertEqual(results['Flq'], 'Qnr-S1')
# self.assertEqual(results['Gly'], '-')
# self.assertEqual(results['MLS'], '-')
# self.assertEqual(results['Ntmdz'], '-')
# self.assertEqual(results['Phe'], '-')
# self.assertEqual(results['Rif'], '-')
# self.assertEqual(results['Sul'], 'SulI')
# self.assertEqual(results['Tet'], 'TetA')
# self.assertEqual(results['Tmt'], 'DfrA1')
# self.assertEqual(results['Omp'], '-')
# self.assertEqual(results['Bla'], 'SHV-110')
# self.assertEqual(results['Bla_Carb'], '-')
# self.assertEqual(results['Bla_ESBL'], '-')
# self.assertEqual(results['Bla_ESBL_inhR'], '-')
# self.assertEqual(results['Bla_broad'], '-')
# self.assertEqual(results['Bla_broad_inhR'], '-')
#
# def test_AS7(self):
# with tempfile.TemporaryDirectory() as tmp_dir:
# contigs = gunzip_contigs_if_necessary('test/test_genomes/AS7.fna.gz', tmp_dir)
# results = self.get_all_results(contigs)
#
# # This genome is missing the start of rmpA, which counts as a truncation to 0%.
# self.assertEqual(results['rmpA'], 'rmpA_1*-0%(KpVP-1)')
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