seismicrna.mask.tests package

Submodules

class seismicrna.mask.tests.main_test.TestMask(*args, **kwargs)

Bases: TestCase, ABC

dataset(*, mask_del: bool = False, mask_ins: bool = False, mask_polya: int = 0, mask_gu: bool = False, mask_discontig: bool = False, min_ncov_read: int = 1, min_finfo_read: float = 0.0, max_fmut_read: float = 1.0, min_mut_gap: int = 0, min_ninfo_pos: int = 1, max_fmut_pos: float = 1.0, **kwargs)

abstract classmethod end3s() → list[list[int]]

3’ end coordinates.

abstract classmethod end5s() → list[list[int]]

5’ end coordinates.

abstract classmethod reads_per_batch() → int

Number of reads per batch.

abstract classmethod reads_per_sample() → dict[str, int]

Number of reads per sample.

setUp()

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

tearDown()

Hook method for deconstructing the test fixture after testing it.

class seismicrna.mask.tests.main_test.TestMask1Batch(*args, **kwargs)

Bases: TestMask, ABC

classmethod reads_per_batch()

Number of reads per batch.

class seismicrna.mask.tests.main_test.TestMask1Sample(*args, **kwargs)

Bases: TestMask, ABC

classmethod reads_per_sample()

Number of reads per sample.

class seismicrna.mask.tests.main_test.TestMask2Samples(*args, **kwargs)

Bases: TestMask, ABC

classmethod reads_per_sample()

Number of reads per sample.

class seismicrna.mask.tests.main_test.TestMaskBatches(*args, **kwargs)

Bases: TestMask, ABC

classmethod reads_per_batch()

Number of reads per batch.

class seismicrna.mask.tests.main_test.TestMaskPaired(*args, **kwargs)

Bases: TestMask, ABC

classmethod end3s()

3’ end coordinates.

classmethod end5s()

5’ end coordinates.

class seismicrna.mask.tests.main_test.TestMaskSingle(*args, **kwargs)

Bases: TestMask, ABC

classmethod end3s()

3’ end coordinates.

classmethod end5s()

5’ end coordinates.

class seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch(*args, **kwargs)

Bases: TestMaskSingle, TestMask1Sample, TestMask1Batch

test_mask_all_muts_min_ncov_read_7()

test_mask_discontig()

test_mask_gu()

test_mask_gu_min_ncov_read_5()

test_mask_gu_min_ncov_read_6()

test_mask_polya_3()

test_mask_polya_4()

test_mask_pos()

test_mask_pos_all()

test_mask_pos_and_mask_pos_file()

test_mask_pos_file()

test_mask_pos_min_ncov_read_5()

test_mask_pos_min_ncov_read_6()

test_mask_pos_multiple()

test_mask_read()

test_mask_read_and_mask_read_file()

test_mask_read_file()

test_min_finfo_read_1()

test_min_ncov_read_6()

test_min_ncov_read_7()

test_min_ncov_read_8()

test_nomask()

seismicrna.mask.tests.main_test.extract_positions(dataset: MaskMutsDataset)

seismicrna.mask.tests.main_test.extract_read_nums(dataset: MaskMutsDataset)

seismicrna.mask.tests.main_test.write_datasets(out_dir: Path, reads_per_sample: dict[str, int], reads_per_batch: int, end5s: list[list[int]], end3s: list[list[int]])