seismicrna.core.tests package

Submodules

class seismicrna.core.tests.array_test.TestCalcInverse(methodName='runTest')

Bases: TestCase

test_calc_inverse(): Invert an array with a known inverse.

test_calc_inverse_fill_fwd(): Invert an array with a known inverse; fill forward.

test_calc_inverse_fill_fwd_max()

test_calc_inverse_fill_fwd_max_default()

test_calc_inverse_fill_rev(): Invert an array with a known inverse; fill reverse.

test_calc_inverse_fill_rev_max()

test_calc_inverse_fill_rev_max_default()

test_calc_inverse_max(): Invert an array with a known inverse.

test_empty()

test_empty_max()

test_is_inverse(): Verify every position in the inverse of a random array.

test_negative(): Negative values in the target are not permitted.

test_repeated(): Repeated values in the target are not permitted.

class seismicrna.core.tests.array_test.TestEnsureSameLength(methodName='runTest')

Bases: TestCase

test_diff_lengths(): Unequal lengths are not permitted.

test_other_dims(): Non-1D arrays are not valid.

test_same_length(): The length is returned when the arrays share the length.

class seismicrna.core.tests.array_test.TestFindDims(methodName='runTest')

Bases: TestCase

test_0d()

test_0d_1dim()

test_0d_none()

test_0d_nonzero()

test_0d_nonzero_extra()

test_1d()

test_1d_0dim_none()

test_1d_1d_crossed()

test_1d_1d_separate()

test_1d_1dim_none()

test_1d_2d_congruent()

test_1d_2d_crossed()

test_1d_2dim()

test_1d_2dim_none()

test_1d_nonzero()

test_2d()

test_2d_1dim_none()

test_2d_2d_congruent()

test_2d_2d_crossed()

test_2d_nonzero()

test_empty()

test_none_2d()

class seismicrna.core.tests.array_test.TestGetLength(methodName='runTest')

Bases: TestCase

test_1d(): A 1D array has a length.

test_other_dims(): Non-1D arrays are not valid.

class seismicrna.core.tests.array_test.TestLocateElements(methodName='runTest')

Bases: TestCase

test_locate_0()

test_locate_1()

test_locate_2()

test_locate_invalid()

class seismicrna.core.tests.array_test.TestTriangular(methodName='runTest')

Bases: TestCase

test_whole_numbers()

class seismicrna.core.tests.header_test.TestClustHeader(methodName='runTest')

Bases: TestCase

test_clustered()

test_clusts()

test_index()

test_iter_clust_indexes()

test_ks_invalid()

test_ks_valid()

test_level_keys()

test_level_names()

test_levels()

test_modified_ks()

test_modified_none()

test_modified_rels()

test_names()

test_num_levels()

test_select_clust()

test_select_clusts()

test_select_extra()

test_select_invalid_clust()

test_select_invalid_k()

test_select_k()

test_select_k_clust_empty()

test_select_k_clust_exist()

test_select_ks()

test_select_ks_clusts_exist()

test_select_none()

test_signature()

class seismicrna.core.tests.header_test.TestConstants(methodName='runTest')

Bases: TestCase

test_average_prefix()

test_clust_name()

test_cluster_prefix()

test_k_name()

test_rel_name()

class seismicrna.core.tests.header_test.TestDeduplicateRels(methodName='runTest')

Bases: TestCase

test_duplicates()

test_empty()

test_no_duplicates()

class seismicrna.core.tests.header_test.TestEqualHeaders(methodName='runTest')

Bases: TestCase

test_clustheaders()

test_different_types()

test_relclustheaders()

test_relheaders()

class seismicrna.core.tests.header_test.TestFormatClustName(methodName='runTest')

Bases: TestCase

test_positive()

test_zero()

class seismicrna.core.tests.header_test.TestFormatClustNames(methodName='runTest')

Bases: TestCase

test_positive_invalid_dups()

test_positive_no_dups()

test_positive_valid_dups()

test_zero()

class seismicrna.core.tests.header_test.TestHeader(methodName='runTest')

Bases: TestCase

test_abstract()

class seismicrna.core.tests.header_test.TestListClusts(methodName='runTest')

Bases: TestCase

test_positive()

test_zero()

class seismicrna.core.tests.header_test.TestListKClusts(methodName='runTest')

Bases: TestCase

test_positive()

test_zero()

class seismicrna.core.tests.header_test.TestListKsClusts(methodName='runTest')

Bases: TestCase

test_empty()

test_ks()

test_one_k()

test_zero()

class seismicrna.core.tests.header_test.TestMakeHeader(methodName='runTest')

Bases: TestCase

test_all()

test_ks()

test_none()

test_rels()

class seismicrna.core.tests.header_test.TestParseHeader(methodName='runTest')

Bases: TestCase

test_clust()

test_empty()

test_extra_index_names()

test_extra_values()

test_invalid_numeric()

test_missing_index_names()

test_missing_values()

test_nonnumeric()

test_rel_index()

test_rel_index_invalid_name()

test_rel_index_repeated()

test_rel_index_valid_name()

test_rel_multiindex()

test_relclust()

class seismicrna.core.tests.header_test.TestRelClustHeader(methodName='runTest')

Bases: TestCase

test_clustered()

test_clusts()

test_index()

test_iter_clust_indexes()

test_ks()

test_level_keys()

test_level_names()

test_levels()

test_modified_all()

test_modified_ks()

test_modified_ks_empty()

test_modified_ks_none()

test_modified_none()

test_modified_nullified()

test_modified_rels()

test_modified_rels_empty()

test_modified_rels_none()

test_num_levels()

test_select_clust()

test_select_extra()

test_select_extra_emptystr()

test_select_extra_none()

test_select_extra_zero()

test_select_invalid_clust()

test_select_invalid_k()

test_select_invalid_rel()

test_select_k_clust_empty()

test_select_k_clust_exist()

test_select_ks()

test_select_none()

test_select_rel()

test_signature()

class seismicrna.core.tests.header_test.TestRelHeader(methodName='runTest')

Bases: TestCase

test_clustered()

test_clusts()

test_index()

test_iter_clust_indexes()

test_ks()

test_level_keys()

test_level_names()

test_levels()

test_modified_ks()

test_modified_none()

test_modified_rels()

test_modified_rels_empty()

test_modified_rels_none()

test_names()

test_num_levels()

test_rels_duplicated()

test_rels_empty()

test_rels_normal()

test_select_extra()

test_select_extra_zero()

test_select_invalid()

test_select_none()

test_select_one_rels()

test_select_rel()

test_select_two_rels()

test_signature()

test_size()

class seismicrna.core.tests.header_test.TestValidateKClust(methodName='runTest')

Bases: TestCase

test_float_clust()

test_float_k()

test_negative_zero()

test_one_zero_allowed()

test_positive_positive()

test_zero()

test_zero_negative()

test_zero_one_allowed()

class seismicrna.core.tests.header_test.TestValidateKs(methodName='runTest')

Bases: TestCase

test_duplicated()

test_empty()

test_valid()

test_zero()

class seismicrna.core.tests.logs_test.TestEraseConfig(methodName='runTest')

Bases: TestCase

test_erase_config()

class seismicrna.core.tests.logs_test.TestExcInfo(methodName='runTest')

Bases: TestCase

test_exc_info()

class seismicrna.core.tests.logs_test.TestGetConfig(methodName='runTest')

Bases: TestCase

test_get_config()

class seismicrna.core.tests.logs_test.TestLevels(methodName='runTest')

Bases: TestCase

test_levels()

class seismicrna.core.tests.logs_test.TestLoggerClass(methodName='runTest')

Bases: TestCase

test_logger_class()

class seismicrna.core.tests.logs_test.TestLoggingRaiseOnError(methodName='runTest')

Bases: TestCase

test_no_raise_on_error()

test_raise_on_error()

class seismicrna.core.tests.logs_test.TestRestoreConfig(methodName='runTest')

Bases: TestCase

test_restore_config_error()

test_restore_config_no_error()

class seismicrna.core.tests.logs_test.TestSetConfig(methodName='runTest')

Bases: TestCase

test_defaults()

test_log_file()

test_no_log_color()

test_raise_on_error()

test_verbosity()

class seismicrna.core.tests.path_test.TestGetSeismicRNASourceDir(methodName='runTest')

Bases: TestCase

test_get_seismicrna_source_dir()

class seismicrna.core.tests.path_test.TestSymlinkIfNeeded(*args, **kwargs)

Bases: TestCase

setUp(): Hook method for setting up the test fixture before exercising it.

tearDown(): Hook method for deconstructing the test fixture after testing it.

test_link_not_symlink()

test_link_valid()

test_link_wrong_symlink()

test_target_not_exist()

class seismicrna.core.tests.random_test.TestStochasticRound(methodName='runTest')

Bases: TestCase

test_float_arrays()

test_float_arrays_preserve_sum()

test_int_arrays()

class seismicrna.core.tests.stats_test.TestCalcBetaMV(methodName='runTest')

Bases: TestCase

test_scipy_beta()

class seismicrna.core.tests.stats_test.TestCalcBetaParams(methodName='runTest')

Bases: TestCase

test_invert()

class seismicrna.core.tests.stats_test.TestCalcDirichletMV(methodName='runTest')

Bases: TestCase

test_scipy_dirichlet()

class seismicrna.core.tests.stats_test.TestCalcDirichletParams(methodName='runTest')

Bases: TestCase

test_invert()

seismicrna.core.tests.stats_test.rand_dirichlet_alpha(n: int): Simulate n alpha parameters for a Dirichlet distribution.

class seismicrna.core.tests.task_test.TestCalcPoolSize(methodName='runTest')

Bases: TestCase

test_1_proc()

test_1_task()

test_multiple()

class seismicrna.core.tests.unbias_test.TestAdjustMinGap(methodName='runTest')

Bases: TestCase

test_gap_le_zero_le_npos()

test_npos_le_zero_le_gap()

test_zero_le_gap_lt_npos()

test_zero_lt_npos_le_gap()

class seismicrna.core.tests.unbias_test.TestCalcPClust(methodName='runTest')

Bases: TestCase

test_p_clust()

class seismicrna.core.tests.unbias_test.TestCalcPClustGivenEndsNoClose(methodName='runTest')

Bases: TestCase

test_calc_p_clust_given_ends_noclose()

class seismicrna.core.tests.unbias_test.TestCalcPClustGivenNoClose(methodName='runTest')

Bases: TestCase

test_ncls1()

test_ncls2()

class seismicrna.core.tests.unbias_test.TestCalcPEnds(methodName='runTest')

Bases: TestCase

test_invert(): Test the inverse of calc_p_ends_given_clust_noclose.

class seismicrna.core.tests.unbias_test.TestCalcPEndsGivenClustNoClose(methodName='runTest')

Bases: TestCase

test_npos0_ncls1()

test_npos1_ncls0()

test_npos1_ncls1()

test_npos2_ncls1()

class seismicrna.core.tests.unbias_test.TestCalcPEndsGivenNoClose(methodName='runTest')

Bases: TestCase

test_calc_p_ends_given_noclose()

class seismicrna.core.tests.unbias_test.TestCalcPEndsObserved(methodName='runTest')

Bases: TestCase

test_calc_p_ends_given_observed()

class seismicrna.core.tests.unbias_test.TestCalcPMutGivenSpan(methodName='runTest')

Bases: TestCase

test_invert(): Test the inverse of calc_p_mut_given_span_noclose.

class seismicrna.core.tests.unbias_test.TestCalcPMutGivenSpanNoClose(methodName='runTest')

Bases: TestCase

test_clusters()

test_simulated()

class seismicrna.core.tests.unbias_test.TestCalcPNoClose(methodName='runTest')

Bases: TestCase

test_p_noclose()

class seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenClust(methodName='runTest')

Bases: TestCase

test_p_noclose_given_clust()

class seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds(methodName='runTest')

Bases: TestCase

Test calc_p_nomut_window and calc_p_noclose_given_ends.

test_clusters()

test_length_0()

test_length_1()

test_length_2_min_gap_1()

test_length_3_min_gap_1()

test_length_3_min_gap_2()

test_length_4_min_gap_1()

test_length_4_min_gap_2()

test_length_4_min_gap_3()

test_min_gap_0()

class seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEndsAuto(methodName='runTest')

Bases: TestCase

test_1_dim()

test_2_dim()

test_invalid_dim()

class seismicrna.core.tests.unbias_test.TestCalcParams(methodName='runTest')

Bases: TestCase

test_infer()

class seismicrna.core.tests.unbias_test.TestCalcRectangularSum(methodName='runTest')

Bases: TestCase

static calc_spanning_sum_slow(array: ndarray)

test_2d()

test_3d()

class seismicrna.core.tests.unbias_test.TestClip(methodName='runTest')

Bases: TestCase

test_with_clip()

test_without_clip()

class seismicrna.core.tests.unbias_test.TestFindSplitPositions(methodName='runTest')

Bases: TestCase

test_0()

test_gap0()

test_gap1_single_end3()

test_gap1_single_end5()

test_gap1_split0_quadruple()

test_gap1_split1_double()

test_gap1_split1_single_mid()

test_gap1_split1_triple()

test_gap1_split2()

test_gap2_single_end3()

test_gap2_single_end5()

test_gap2_split0()

test_gap2_split1()

test_gap3_single_end3()

test_gap3_single_end5()

test_gap4_split0()

test_gap4_split1()

test_generic_split()

test_thresh0()

test_thresh1()

class seismicrna.core.tests.unbias_test.TestNoCloseMuts(methodName='runTest')

Bases: TestCase

test_more_muts()

test_no_muts()

test_one_mut()

class seismicrna.core.tests.unbias_test.TestNormalize(methodName='runTest')

Bases: TestCase

test_sum_positive()

test_sum_zero()

class seismicrna.core.tests.unbias_test.TestQuickUnbias(methodName='runTest')

Bases: TestCase

Test that the quick unbiasing algorithm produces results very similar to the exact algorithm.

ABS_TOL = 0.0005

REL_TOL = 0.03

static random_params(npos: int, ncls: int)

test_threshold_0()

test_threshold_0p001()

class seismicrna.core.tests.unbias_test.TestSlicePEnds(methodName='runTest')

Bases: TestCase

test_0x0()

test_slice_3x3()

test_slice_5x5()

class seismicrna.core.tests.unbias_test.TestTriuAllClose(methodName='runTest')

Bases: TestCase

test_equal()

test_float_equal()

test_float_unequal()

test_tril()

test_triu()

class seismicrna.core.tests.unbias_test.TestTriuCumSum(methodName='runTest')

Bases: TestCase

test_1x1x2()

test_2x2()

test_2x2x1()

test_2x2x2()

test_3x3()

test_all_0()

test_all_1()

test_explicit_sum()

class seismicrna.core.tests.unbias_test.TestTriuDiv(methodName='runTest')

Bases: TestCase

test_1x1()

test_1x1x1()

test_2x2()

test_2x2x2()

class seismicrna.core.tests.unbias_test.TestTriuDot(methodName='runTest')

Bases: TestCase

test_1x1()

test_1x1x1()

test_2x2()

test_2x2x2()

class seismicrna.core.tests.unbias_test.TestTriuLog(methodName='runTest')

Bases: TestCase

compare(result: ndarray, expect: ndarray)

test_2d()

test_3d()

class seismicrna.core.tests.unbias_test.TestTriuMul(methodName='runTest')

Bases: TestCase

test_1x1()

test_1x1x1()

test_2x2()

test_2x2x2()

class seismicrna.core.tests.unbias_test.TestTriuNorm(methodName='runTest')

Bases: TestCase

compare(result: ndarray, expect: ndarray)

test_0x0()

test_0x0x1()

test_1x1()

test_1x1x1()

test_1x1x2()

test_2x2()

test_2x2_zero()

test_2x2x1()

test_2x2x2()

test_2x2x2_zero()

test_2x2x2x2()

test_2x2x2x2_zero()

class seismicrna.core.tests.unbias_test.TestTriuSum(methodName='runTest')

Bases: TestCase

test_1x1()

test_1x1x1()

test_1x1x2()

test_2x2()

test_2x2x1()

test_2x2x2()

test_2x2x2x2()

test_all_zero()

seismicrna.core.tests.unbias_test.label_no_close_muts(muts: ndarray, min_gap: int): Return a 1D vector that is True for every row in muts that has no two mutations that are too close, otherwise False.

seismicrna.core.tests.unbias_test.no_close_muts(read: ndarray, min_gap: int): Return True if the read has no two mutations separated by fewer than min_gap non-mutated positions, otherwise False.

seismicrna.core.tests.unbias_test.simulate_params(n_pos: int, n_cls: int, p_mut_max: float = 1.0): Return p_mut, p_ends, and p_clust parameters.

seismicrna.core.tests.unbias_test.simulate_reads(n_reads: int, p_mut: ndarray, p_ends: ndarray): Simulate n_reads reads based on the mutation rates (p_mut) and the distributions of end coordinates (p_ends).

class seismicrna.core.tests.version_test.TestConsistentVersion(methodName='runTest')

Bases: TestCase

test_meson_build()

class seismicrna.core.tests.version_test.TestFormatVersion(methodName='runTest')

Bases: TestCase

test_format_default()

test_format_notag()

test_format_prtag()

class seismicrna.core.tests.version_test.TestParseVersion(methodName='runTest')

Bases: TestCase

test_invalid_1()

test_invalid_2()

test_invalid_3()

test_invalid_4()

test_invalid_5()

test_parse_default()

test_parse_notag()

test_parse_prtag_letter()

test_parse_prtag_letters()

test_parse_prtag_letters_numbers()