def generate_UMIs(): np.random.seed(123) pool = ampcycle.Pool() pool.createUMIsWithBias(100, 0.7, 1, 0.001) pool.SimulateCycleWithErrors() pool.PCRcyclesWithErrorsAndBias(5) return pool
def test_SimulateCycleWithErrors(): pool = ampcycle.Pool() pool.createUMIsWithBias(10, 1, 1, 0) pool.SimulateCycleWithErrors() assert len(pool.umis_amplified.keys()) == 10 assert sum(pool.umis_amplified.values()) == 20
def test_addSequencingErrors(): pool = ampcycle.Pool() pool.createUMIsWithBias(10, 1, 1, 0) pool.SimulateCycleWithErrors() pool.addSequencingErrors() assert len(pool.umis_amplified.keys()) >= 10
def test_downsampleUMIs(): pool = ampcycle.Pool() pool.createUMIsWithBias(10, 1, 1, 0) pool.SimulateCycleWithErrors() pool.downsampleUMIs(0.1) assert len(pool.umis_amplified.keys()) <= 10
def test_createUMIsWithBias(): pool = ampcycle.Pool() pool.createUMIsWithBias(10) assert len(pool.umis.keys()) == 10
def test_PCRcyclesWithErrorsAndBias(): pool = ampcycle.Pool() pool.createUMIsWithBias(10, 1, 1, 0) pool.SimulateCycleWithErrors() pool.PCRcyclesWithErrorsAndBias(2) assert sum(pool.umis_amplified.values()) == 80