seismicrna.tests package
Submodules
- class seismicrna.tests.ensembles_test.TestAggregatePairs(methodName='runTest')
Bases:
TestCase- test_one()
- test_three_disjoint()
- test_three_nested()
- test_three_serial()
- test_two_disjoint()
- test_two_nested()
- test_two_serial()
- test_zero()
- class seismicrna.tests.ensembles_test.TestCalcModulesFromPairs(methodName='runTest')
Bases:
TestCase- test_1_module()
- test_2_modules()
- test_split_modules()
- class seismicrna.tests.ensembles_test.TestCalcNullSpanPerPosKeepDists(methodName='runTest')
Bases:
TestCase- test_multiple_reads()
- test_no_pairs()
- test_ref_1_read_1()
- test_ref_4_read_1()
- test_ref_4_read_2()
- test_ref_4_read_3()
- test_ref_4_read_4()
- test_ref_5_read_1()
- test_ref_5_read_2()
- test_ref_5_read_3()
- test_ref_5_read_4()
- test_ref_5_read_5()
- class seismicrna.tests.ensembles_test.TestCalcNullSpanPerPosRandDists(methodName='runTest')
Bases:
TestCase- test_1_pair()
- test_2_pairs()
- test_no_pairs()
- class seismicrna.tests.ensembles_test.TestCalcSpanPerPos(methodName='runTest')
Bases:
TestCase- test_calc_span_per_pos()
- class seismicrna.tests.ensembles_test.TestCalcTiles(methodName='runTest')
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_region_not_divisible()
- test_tile_length_larger()
- test_tile_min_overlap_25()
- test_tile_min_overlap_75()
- test_total_tile_length_1()
- class seismicrna.tests.ensembles_test.TestEnsembles(methodName='runTest')
Bases:
TestCase- MODULES = [('TGACGAACAACGTGTTTGTGAACCATATAGGTAAACGCTGAATGCGTTCGCGCGGAGGGT', ['..(((((((...)))))))..(((......((.(((((.....))))).))......)))', '...(((...(((((((((((.(((.....)))...))).))))))))))).((.....))']), ('TTTGCAGGAAGATGGTCAACTCTACACCTAGTTTTTACCAGTCCACAAGAGTTTGAACTG', ['.(((..(((...((((.((..(((....)))..)).)))).))).))).(((....))).']), ('GTGCCTTAACCTGAGTACGCCCATATCATGGGAGACATTACAACTCAAATTCTAGGTGTG', ['..((((.....(((((...(((((...)))))..........)))))......))))...', '((((.(((...)))))))...((((((.((((..................))))))))))'])]
- PROFILE = 'ensembles'
- REF = 'test_ref'
- REFS = 'test_refs'
- SAMPLE = 'test_sample'
- SIM_DIR = PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/sim')
- run_ensembles(relate_dirs: list[Path], expect_regions: dict[tuple[int, int], int], tolerance: int = 0, **kwargs)
- setUp()
Hook method for setting up the test fixture before exercising it.
- tearDown()
Hook method for deconstructing the test fixture after testing it.
- test_modules012_read120()
- test_modules012_read180()
- test_modules012_read60()
- test_modules02_read60()
- class seismicrna.tests.ensembles_test.TestExpandRegionsIntoGaps(methodName='runTest')
Bases:
TestCase- test_one()
- test_two()
- test_zero()
- class seismicrna.tests.ensembles_test.TestFilterModulesLength(methodName='runTest')
Bases:
TestCase- test_filter_default_length()
- test_filter_max_length()
- test_filter_min_length()
- class seismicrna.tests.ensembles_test.TestInsertRegionsIntoGaps(methodName='runTest')
Bases:
TestCase- test_one()
- test_two()
- test_zero()
- class seismicrna.tests.ensembles_test.TestSelectPairs(methodName='runTest')
Bases:
TestCase- test_select_pairs()
- class seismicrna.tests.wf_test.TestWorkflow(methodName='runTest')
Bases:
TestCase- OUT_DIR = PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/wf-test-out')
- SIM_DIR = PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/wf-test-sim')
- setUp()
Hook method for setting up the test fixture before exercising it.
- tearDown()
Hook method for deconstructing the test fixture after testing it.
- test_wf_sim_2samples_2refs_20000reads_2clusts()
- class seismicrna.tests.wf_test.TestWorkflowTwoOutDirs(methodName='runTest')
Bases:
TestCase- CJOINED = 'cjoined_region'
- MJOINED = 'mjoined_region'
- NUMBERS = [1, 2]
- OUT_DIR = PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/wf2-test-out')
- OUT_DIRS = (PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/wf2-test-out1'), PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/wf2-test-out2'))
- POOLED = 'pooled_sample'
- REF = 'test_ref'
- REFS = 'test_refs'
- SAMPLE = 'test_sample'
- SIM_DIR = PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/wf2-test-sim')
- SIM_DIRS = (PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/wf2-test-sim1'), PosixPath('/home/runner/work/seismic-rna/seismic-rna/src/userdocs/wf2-test-sim2'))
- check_no_identical(files: Iterable[str | Path], binary: bool)
Confirm no two files have identical contents.
- setUp()
Hook method for setting up the test fixture before exercising it.
- tearDown()
Hook method for deconstructing the test fixture after testing it.
- test_wf_two_out_dirs()