def test_bowtie_with_other_mixture(self, env_mock, path_mock):
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {'SRST2_BOWTIE2_BUILD': '/usr/bin/bowtie2-build'}
env_mock.get.side_effect = fake_env_variables.get
bowtie_exec, bowtie_build_exec = srst2.get_bowtie_execs()
self.assertEqual(bowtie_exec, 'bowtie2')
self.assertEqual(bowtie_build_exec, '/usr/bin/bowtie2-build')
def test_bowtie_with_other_mixture(self, env_mock, path_mock):
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {'SRST2_BOWTIE2_BUILD': '/usr/bin/bowtie2-build'}
env_mock.get.side_effect = fake_env_variables.get
bowtie_exec, bowtie_build_exec = srst2.get_bowtie_execs()
self.assertEqual(bowtie_exec, 'bowtie2')
self.assertEqual(bowtie_build_exec, '/usr/bin/bowtie2-build')
def test_bowtie_with_defaults(self, env_mock, path_mock):
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {}
env_mock.get.side_effect = fake_env_variables.get
bowtie_exec, bowtie_build_exec = srst2.get_bowtie_execs()
self.assertEqual(bowtie_exec, 'bowtie2')
self.assertEqual(bowtie_build_exec, 'bowtie2-build')
def test_bowtie_with_defaults(self, env_mock, path_mock):
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {}
env_mock.get.side_effect = fake_env_variables.get
bowtie_exec, bowtie_build_exec = srst2.get_bowtie_execs()
self.assertEqual(bowtie_exec, 'bowtie2')
self.assertEqual(bowtie_build_exec, 'bowtie2-build')
