def test_bad_aligner_parameter_raises_exception(self):
"""
Pass a aligner parameter that is not specified in the aligners config file
"""
available_aligners = ('star', 'snapr')
default_aligner = 'star'
# create a PipelineBuilder and add mocked pipeline/project objects as patches
p = PipelineBuilder('/path/to/dir')
mock_pipeline_params = Params()
mock_pipeline_params.add(available_aligners = available_aligners,
default_aligner = default_aligner,
aligner='junk')
p.builder_params = mock_pipeline_params
p._PipelineBuilder__get_aligner_info = mock.Mock()
with self.assertRaises(IncorrectAlignerException):
p._PipelineBuilder__check_aligner_valid()
def test_missing_aligner_config_file_raises_exception(self, mock_os):
available_aligners = ('star', 'snapr')
default_aligner = 'star'
# create a PipelineBuilder and add mocked pipeline/project objects as patches
p = PipelineBuilder('/path/to/dir')
mock_pipeline_params = Params()
mock_pipeline_params.add(available_aligners=available_aligners,
default_aligner=default_aligner,
aligner=None,
aligners_dir='/path/to/dir',
genome='mm9')
p.builder_params = mock_pipeline_params
p._PipelineBuilder__get_aligner_info = mock.Mock()
mock_os.listdir.return_value = []
with self.assertRaises(ConfigFileNotFoundException):
p._PipelineBuilder__check_aligner_valid()
def test_default_aligner_used_when_not_specified(self, mock_os):
"""
If no commandline arg given for aligner, check that it resorts to the default
"""
available_aligners = ('star', 'snapr')
default_aligner = 'star'
# create a PipelineBuilder and add mocked pipeline/project objects as patches
p = PipelineBuilder('/path/to/dir')
mock_pipeline_params = Params()
mock_pipeline_params.add(available_aligners = available_aligners,
default_aligner = default_aligner,
aligner=None,
aligners_dir = '/path/to/dir',
genome = 'hg19')
p.builder_params = mock_pipeline_params
p.all_components = []
p._PipelineBuilder__get_aligner_info = mock.Mock()
mock_os.listdir.return_value = ['star.cfg']
p._PipelineBuilder__check_aligner_valid()
self.assertEqual(p.builder_params.get('aligner'), default_aligner)