seismicrna.sim.tests package

Submodules

class seismicrna.sim.tests.abstract_test.AbstractTestBase(methodName='runTest')

Bases: TestCase

Silence logging during tests; subclasses get tmpdirs as needed.

classmethod setUpClass()

Hook method for setting up class fixture before running tests in the class.

classmethod tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

class seismicrna.sim.tests.abstract_test.FakeFilterPositionTable(*, top: Path, sample: str, ref: str, refseq: DNA, reg: str, clusts: list[tuple[int, int]], counts_per_clust: dict[tuple[int, int], DataFrame])

Bases: object

Duck-typed FilterPositionTable for abstract_table tests.

Only the attributes that abstract_table reads are implemented.

property branches: dict

fetch_count(*, k: int, clust: int) → DataFrame

iter_profiles(*, fold_table_region=True, regions=None, **kwargs)

property reg: str

class seismicrna.sim.tests.abstract_test.FakeHeader(clusts)

Bases: object

class seismicrna.sim.tests.abstract_test.TestAbstractTable(methodName='runTest')

Bases: AbstractTestBase

DB_STRING = '((....))'

REF = 'ref'

REFSEQ = DNA('ACGTACGT')

REG = 'myreg'

SAMPLE = 'sample'

setUp()

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

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_clustered_multiple_ct_files()

test_min_aucroc_skips_cluster()

test_missing_cluster_ct_file_uses_only_available()

test_no_ct_files_returns_empty()

test_no_matching_ct_ref_skips_profile()

test_no_matching_ct_reg_skips_profile()

test_non_clustered_auto_detect()

test_non_clustered_with_explicit_struct_file()

class seismicrna.sim.tests.abstract_test.TestAccumulateRatios(methodName='runTest')

Bases: AbstractTestBase

test_accumulates_from_empty()

test_concatenates_arrays_per_key()

test_three_inputs_compound()

class seismicrna.sim.tests.abstract_test.TestCalcRatioStats(methodName='runTest')

Bases: AbstractTestBase

MARGIN = 1e-06

test_fvar_falls_back_to_margin_when_too_few_values()

test_fvar_keys_are_acgt()

test_fvar_known_values()

test_fvar_omits_n_base()

test_mean_clipped_to_margin_when_zero()

test_mean_clipped_to_upper_bound()

class seismicrna.sim.tests.abstract_test.TestCalcRatios(methodName='runTest')

Bases: AbstractTestBase

Verify _calc_ratios computes per-position ratios analytically.

REFSEQ = DNA('ACGTACGT')

test_loq_paired_vs_unpaired()

test_per_base_mutation_rate_xm()

test_per_base_substitution_ratios()

test_unpaired_collects_only_unpaired_positions()

class seismicrna.sim.tests.abstract_test.TestEndToEndComposition(methodName='runTest')

Bases: AbstractTestBase

DB_STRING = '((....))'

REF = 'ref'

REFSEQ = DNA('ACGTACGT')

setUp()

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

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_four_tables_accumulate()

test_single_table()

test_two_tables_accumulate()

class seismicrna.sim.tests.abstract_test.TestFormatParamTokens(methodName='runTest')

Bases: AbstractTestBase

Guard against regressions where sim abstract emits parameters that make_pmut_means does not accept (e.g. pnd).

test_all_other_keys_still_emitted()

test_emitted_tokens_round_trip_to_make_pmut_means()

class seismicrna.sim.tests.cli_test.TestSimCLIInvocation(methodName='runTest')

Bases: TestCase

Smoke-test each subcommand via CliRunner.

Two tiers:

• –help: validates Click’s param parsing and help-text generation for every command (including fold, which needs a positional arg).

• empty invocation ([]): calls run() through the full decorator stack with no files; commands return empty results with exit_code 0. fold is excluded because its positional arg is required and Click itself rejects an empty invocation with exit_code 2.

setUp()

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

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_abstract_empty()

test_abstract_help()

test_clusts_empty()

test_clusts_help()

test_ends_empty()

test_ends_help()

test_fastq_empty()

test_fastq_help()

test_fold_help()

test_idmut_empty()

test_idmut_help()

test_muts_empty()

test_muts_help()

test_params_empty()

test_params_help()

test_ref_empty()

test_ref_help()

test_total_empty()

test_total_help()

class seismicrna.sim.tests.cli_test.TestSimCLIParams(methodName='runTest')

Bases: TestCase

Check every CLI param name appears in run()’s signature.

inspect.signature() follows the __wrapped__ chain (all decorators in run_func use @wraps) and stops at the __signature__ set by param_defaults, which preserves the original parameter names.

test_abstract()

test_clusts()

test_ends()

test_fastq()

test_fold()

test_idmut()

test_muts()

test_params()

test_ref()

test_total()

class seismicrna.sim.tests.ends_test.TestSimPEnds(methodName='runTest')

Bases: TestCase

equate(end5: int, end3: int, center_fmean: float, center_fvar: float, length_fmean: float, length_fvar: float, end5s: ndarray, end3s: ndarray, pends: ndarray, **kwargs)

test_center_fvar_0_length_fvar_0()

test_zero_length_1_to_0_keep()

test_zero_length_9_to_8_drop()

test_zero_length_9_to_8_keep()

class seismicrna.sim.tests.idmut_test.TestParseMinMutGapWeights(methodName='runTest')

Bases: TestCase

test_duplicate_gap()

test_empty_string()

test_gap_float_string()

test_gap_not_integer()

test_multiple_pairs()

test_multiple_zero_weights_excluded()

test_negative_gap()

test_negative_weight()

test_output_sorted_by_gap()

test_pair_extra_colon()

test_pair_missing_colon()

test_single_pair_gap0()

test_single_pair_nonzero_gap()

test_single_pair_weight_zero_invalid()

test_weight_above_1()

test_weight_not_float()

test_weights_do_not_sum_to_1()

test_weights_exceed_1_in_total()

test_weights_sum_to_1_within_float_tolerance()

test_zero_weight_excluded()

class seismicrna.sim.tests.idmut_test.TestSimulateBatches(methodName='runTest')

Bases: TestCase

AMB = 129

NUM_READS = 10000000

PCLUST = [0.2, 0.5, 0.3]

P_GAP = {0: 0.2, 5: 0.3, 15: 0.5}

TOLERANCE = 0.005

test_drop_read_counts_single_gap()

Single-gap DROP path must yield ~num_reads final reads.

test_read_counts_with_gap_weights()