seismicrna.tests package

Submodules

class seismicrna.tests.ensembles_test.TestCalcRegions(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_length_larger()

test_region_min_overlap_25()

test_region_min_overlap_75()

test_region_not_divisible()

test_total_region_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], region_length: int, region_min_overlap: float, expect_ks: list[int], expect_regions: list[list[str]], **kwargs)

setUp()

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

classmethod sim_data(module_nums: list[int], read_length: int)

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.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()

seismicrna.tests.wf_test.list_actions(num_structs: int)

seismicrna.tests.wf_test.list_profiles(num_structs: int)

seismicrna.tests.wf_test.list_step_dir_contents(parent_dir: Path, step: str, num_batches: int, write_read_names: bool = True)