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()
]
