def test_run_bowtie_with_overide(self, env_mock, path_mock, run_mock,
version_mock, logging_mock):
fake_env_variables = {
'SRST2_SAMTOOLS': '/usr/bin/samtools',
'SRST2_BOWTIE2': '/usr/bin/bowtie2',
'SRST2_BOWTIE2_BUILD': '/usr/bin/bowtie2-build'
}
env_mock.get.side_effect = fake_env_variables.get
path_mock.isfile.side_effect = lambda f: 'missing' not in f
arg_mock = MagicMock()
arg_mock.read_type = 'foo'
arg_mock.stop_after = False
arg_mock.other = False
arg_mock.threads = 4
arg_mock.use_existing_bowtie2_sam = False
actual_sam = srst2.run_bowtie('mapping_file', 'sample', ['fastq'],
arg_mock, 'db_name', 'db_path')
self.assertEqual(actual_sam, 'mapping_file.sam')
self.assertEqual(version_mock.call_count, 2)
self.assertEqual(version_mock.call_args_list[0][0][0],
['/usr/bin/bowtie2', '--version'])
self.assertEqual(version_mock.call_args_list[1][0][0],
['/usr/bin/samtools'])
expected_bowtie2_command = [
'/usr/bin/bowtie2', '-U', 'fastq', '-S', 'mapping_file.sam',
'-foo', '--very-sensitive-local', '--no-unal', '-a', '-x',
'db_path', '--threads', '4'
]
run_mock.assert_called_once_with(expected_bowtie2_command)
def test_run_bowtie_with_defaults(self, env_mock, path_mock, run_mock,
version_mock, logging_mock):
fake_env_variables = {}
env_mock.get.side_effect = fake_env_variables.get
path_mock.isfile.side_effect = lambda f: 'missing' not in f
arg_mock = MagicMock()
arg_mock.read_type = 'foo'
arg_mock.stop_after = False
arg_mock.other = False
arg_mock.threads = 4
arg_mock.use_existing_bowtie2_sam = False
actual_sam = srst2.run_bowtie('mapping_file', 'sample', ['fastq'], arg_mock,
'db_name', 'db_path')
self.assertEqual(actual_sam, 'mapping_file.sam')
self.assertEqual(version_mock.call_count, 2)
self.assertEqual(version_mock.call_args_list[0][0][0], ['bowtie2',
'--version'])
self.assertEqual(version_mock.call_args_list[1][0][0], ['samtools'])
expected_bowtie2_command = [
'bowtie2',
'-U', 'fastq',
'-S', 'mapping_file.sam',
'-foo',
'--very-sensitive-local',
'--no-unal',
'-a',
'-x', 'db_path',
'--threads', '4'
]
run_mock.assert_called_once_with(expected_bowtie2_command)
def test_run_bowtie_with_defaults(self, env_mock, path_mock, run_mock,
version_mock, logging_mock):
fake_env_variables = {}
env_mock.get.side_effect = fake_env_variables.get
path_mock.isfile.side_effect = lambda f: 'missing' not in f
arg_mock = MagicMock()
arg_mock.read_type = 'foo'
arg_mock.stop_after = False
arg_mock.other = False
actual_sam = srst2.run_bowtie('mapping_file', 'sample', ['fastq'],
arg_mock, 'db_name', 'db_path')
self.assertEqual(actual_sam, 'mapping_file.sam')
self.assertEqual(version_mock.call_count, 2)
self.assertEqual(version_mock.call_args_list[0][0][0],
['bowtie2', '--version'])
self.assertEqual(version_mock.call_args_list[1][0][0], ['samtools'])
expected_bowtie2_command = [
'bowtie2', '-U', 'fastq', '-S', 'mapping_file.sam', '-foo',
'--very-sensitive-local', '--no-unal', '-a', '-x', 'db_path'
]
run_mock.assert_called_once_with(expected_bowtie2_command)
