def test_bowtie_index_with_default(self, env_mock, path_mock, run_mock, version_mock, stdout_mock): path_mock.exists.return_value = False env_mock.get.return_value = None slurm_srst2.bowtie_index(['foo']) self.assertEqual(version_mock.call_count, 1) self.assertEqual(version_mock.call_args[0][0], ['bowtie2', '--version']) self.assertEqual(run_mock.call_count, 1) run_mock.assert_called_once_with(['bowtie2-build', 'foo', 'foo'])
def test_bowtie_index_with_default(self, env_mock, path_mock, run_mock,
version_mock, stdout_mock):
path_mock.exists.return_value = False
env_mock.get.return_value = None
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0],
['bowtie2', '--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['bowtie2-build', 'foo', 'foo'])
def test_bowtie_index_with_partial_overide(self, env_mock, path_mock, run_mock,
version_mock, stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
fake_env_variables = {'SRST2_BOWTIE2': '/usr/bin/bowtie2'}
env_mock.get.side_effect = fake_env_variables.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['/usr/bin/bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['/usr/bin/bowtie2-build', 'foo', 'foo'])
def test_bowtie_index_with_missing_overide(self, env_mock, path_mock,
run_mock, version_mock,
stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
env_mock.get.side_effect = {'SRST2_SAMTOOLS': '/missing/bowtie'}.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0], ['bowtie2',
'--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['bowtie2-build', 'foo', 'foo'])
def test_bowtie_index_with_missing_overide(self, env_mock, path_mock,
run_mock, version_mock,
stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: 'missing' not in f
env_mock.get.side_effect = {'SRST2_SAMTOOLS': '/missing/bowtie'}.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0],
['bowtie2', '--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['bowtie2-build', 'foo', 'foo'])
def test_bowtie_index_with_missing_inference(self, env_mock, path_mock,
run_mock, version_mock,
stdout_mock):
path_mock.exists.return_value = False
path_mock.isfile.side_effect = lambda f: f == '/usr/bin/bowtie2'
fake_env_variables = {'SRST2_BOWTIE2': '/usr/bin/bowtie2'}
env_mock.get.side_effect = fake_env_variables.get
slurm_srst2.bowtie_index(['foo'])
self.assertEqual(version_mock.call_count, 1)
self.assertEqual(version_mock.call_args[0][0],
['/usr/bin/bowtie2', '--version'])
self.assertEqual(run_mock.call_count, 1)
run_mock.assert_called_once_with(['bowtie2-build', 'foo', 'foo'])
