def test_ttest(): data1 = {'BAD': 1.2345, 'FUCA2': 6.5432} data2 = {'BAD': 2.3456, 'FUCA2': 7.6543} data3 = {'BAD': 6.3456, 'FUCA2': 11.6543} data4 = {'BAD': 7.1111, 'FUCA2': 9.9711} tumour_samples = [Sample.from_names('Tumour_1', data1), Sample.from_names('Tumour_2', data2)] normal_samples = [Sample.from_names('Normal_1', data3), Sample.from_names('Normal_2', data4)] tumour = SampleCollection('Tumour', tumour_samples) normal = SampleCollection('Normal', normal_samples) experiment = Experiment(case=tumour, control=normal) tt = ttest(experiment) assert isinstance(tt, pd.Series) assert all(gene in list(tt.keys()) for gene in experiment.get_all().genes)
def test_sample_from_names(): data = {'BAD': 1.2345, 'FUCA2': 6.5432} sample = Sample.from_names('Tumour_1', data) assert sample.name == 'Tumour_1' assert all(isinstance(k, Gene) for k in sample.data.keys()) assert [k.name for k in sample.data.keys()] == ['BAD', 'FUCA2'] assert all(isinstance(v, float) for v in sample.data.values()) assert list(sample.data.values()) == [1.2345, 6.5432]
def test_get_all(): data1 = {'BAD': 1.2345, 'FUCA2': 6.5432} data2 = {'BAD': 2.3456, 'FUCA2': 7.6543} data3 = {'BAD': 3.4567} tumour_samples = [ Sample.from_names('Tumour_1', data1), Sample.from_names('Tumour_2', data2) ] normal_samples = [Sample.from_names('Normal_1', data3)] tumour = SampleCollection('Tumour', tumour_samples) normal = SampleCollection('Normal', normal_samples) experiment_samples = Experiment(case=tumour, control=normal).get_all() assert isinstance(experiment_samples, SampleCollection) assert all(label in experiment_samples.labels for label in tumour.labels + normal.labels)
def test_init(): data1 = {'BAD': 1.2345, 'FUCA2': 6.5432} data2 = {'BAD': 2.3456, 'FUCA2': 7.6543} data3 = {'BAD': 3.4567} tumour_samples = [ Sample.from_names('Tumour_1', data1), Sample.from_names('Tumour_2', data2) ] normal_samples = [Sample.from_names('Normal_1', data3)] tumour = SampleCollection('Tumour', tumour_samples) normal = SampleCollection('Normal', normal_samples) experiment = Experiment(case=tumour, control=normal) assert isinstance(experiment.case, SampleCollection) assert isinstance(experiment.control, SampleCollection) assert experiment.case == tumour assert experiment.control == normal
def make_samples(samples_dict): """Create samples from dict representation""" return [ Sample.from_names(name, values) for name, values in samples_dict.items() ]