def test_creates_contrasts_correctly_with_no_contrast_file_given(self):
#make some samples:
all_samples = [Sample('A', 'X'), Sample('B', 'Y'), Sample('C', 'Z')]
p = PipelineBuilder('')
mock_pipeline_params = Params()
mock_pipeline_params.add(skip_analysis = False)
mock_pipeline_params.add(contrast_file = None)
p.builder_params = mock_pipeline_params
p.all_samples = all_samples
p._PipelineBuilder__check_contrast_file()
expected_result = set([('X','Y'),('X','Z'),('Y','Z')])
self.assertTrue(set_of_tuples_is_equivalent(p.contrasts, expected_result))
def test_raises_exception_if_non_sensible_contrast_specified(self, mock_parse):
#make some samples:
all_samples = [Sample('A', 'X'), Sample('B', 'Y'), Sample('C', 'Z')]
p = PipelineBuilder('')
mock_pipeline_params = Params()
mock_pipeline_params.add(skip_analysis = False)
mock_pipeline_params.add(contrast_file = 'contrast.txt')
p.builder_params = mock_pipeline_params
p.all_samples = all_samples
# note the specification of a contrast of Y against A. However, we have no samples from condition A.
mock_parse.return_value = set([('X','Y'),('X','Z'),('Y','A')])
with self.assertRaises(ContrastSpecificationException):
p._PipelineBuilder__check_contrast_file()