seismicrna.cluster.tests package

Submodules

class seismicrna.cluster.tests.emk_test.TestAssignClusterings(methodName='runTest')

Bases: TestCase

compare_result(x: ndarray, y: ndarray, expect: ndarray)

test_0_clusters()

test_0_positions()

test_1_cluster()

test_more_clusters()

class seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores(*args, **kwargs)

Bases: TestCase

REF = 'test_ref'

REFS = 'test_refs'

SAMPLE = 'test_sample'

SIM_DIR = PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/test_sim')

static calc_confidence_interval(log_jackpot_quotients: list[float], confidence_level: float)

setUp()

Hook method for setting up the test fixture before exercising it.

sim_jackpot_quotient()

Simulate a dataset and return its jackpotting quotient.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_ideal_jackpot()

Test that bootstrapping “perfect” data correctly returns a jackpotting quotient that is expected to be 1.

class seismicrna.cluster.tests.jackpot_test.TestCalcSemiGAnomaly(methodName='runTest')

Bases: TestCase

test_array_all_equal()

test_array_all_unequal()

test_float_equal()

test_float_unequal()

class seismicrna.cluster.tests.jackpot_test.TestSimClusters(methodName='runTest')

Bases: TestCase

test_sim_clusters()

class seismicrna.cluster.tests.jackpot_test.TestSimReads(methodName='runTest')

Bases: TestCase

static count_reads(reads: ndarray, clusts: ndarray, n_clust: int)

Count reads for each cluster and position.

test_sim_reads()

class seismicrna.cluster.tests.marginal_test.TestMarginalResps(methodName='runTest')

Bases: TestCase

compare(p_mut: ndarray, p_ends: ndarray, p_clust: ndarray, end5s: ndarray, end3s: ndarray, unmasked: ndarray, muts_per_pos: list[ndarray], min_mut_gap: int, expect_log_marginals: ndarray, expect_resps: ndarray)

test_1pos()

test_1pos_2clusters()

test_2pos_gap0()

test_2pos_gap0_2clusters()

test_2pos_gap1()

test_2pos_masked0()

test_2pos_masked1()