# Path: kleborate/__main__.py
# def get_iro_mlst_results(data_folder, contigs, args):
#     return get_virulence_cluster_results(data_folder, contigs, 'iro_alleles.fasta',
#                                          'SmST_profiles.txt', 'Salmochelin', 'SmST',
#                                          'iro unknown', 2, get_iro_mlst_header, args)


import collections
import unittest
from kleborate.__main__ import get_iro_mlst_results
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/>.
"""




class TestIro(unittest.TestCase):
    """
    Tests salmochelin ST calls.
    """

    def setUp(self):
        self.data_dir = 'test/test_iro/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_iro_random(self):
        """
        This test has just random sequence and should give no iro call.
        """

# Path: kleborate/__main__.py
# def get_iro_mlst_results(data_folder, contigs, args):
#     return get_virulence_cluster_results(data_folder, contigs, 'iro_alleles.fasta',
#                                          'SmST_profiles.txt', 'Salmochelin', 'SmST',
#                                          'iro unknown', 2, get_iro_mlst_header, args)


# Path: test/test_iro.py
import collections
import unittest
from kleborate.__main__ import get_iro_mlst_results

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/>.
"""




class TestIro(unittest.TestCase):
    """
    Tests salmochelin ST calls.
    """

    def setUp(self):
        self.data_dir = 'test/test_iro/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_iro_random(self):
        """
        This test has just random sequence and should give no iro call.
        """

        results = get_iro_mlst_results(self.data_dir, 'test/test_iro/test_random.fasta', self.args)