seismicrna.filter.tests package
Submodules
- class seismicrna.filter.tests.main_test.TestFilter(*args, **kwargs)
Bases:
TestCase,ABC- dataset(*, count_del: bool = True, count_ins: bool = True, mask_polya: int = 0, probe: str = 'none', mask_a: bool | None = None, mask_c: bool | None = None, mask_g: bool | None = None, mask_u: bool | None = None, drop_discontig: bool = False, min_ncov_read: int = 1, min_fcov_read: float = 0.0, 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)
- 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.filter.tests.main_test.TestFilter1Batch(*args, **kwargs)
Bases:
TestFilter,ABC- classmethod reads_per_batch()
Number of reads per batch.
- class seismicrna.filter.tests.main_test.TestFilter1Sample(*args, **kwargs)
Bases:
TestFilter,ABC- classmethod reads_per_sample()
Number of reads per sample.
- class seismicrna.filter.tests.main_test.TestFilter2Samples(*args, **kwargs)
Bases:
TestFilter,ABC- classmethod reads_per_sample()
Number of reads per sample.
- class seismicrna.filter.tests.main_test.TestFilterBatches(*args, **kwargs)
Bases:
TestFilter,ABC- classmethod reads_per_batch()
Number of reads per batch.
- class seismicrna.filter.tests.main_test.TestFilterPaired(*args, **kwargs)
Bases:
TestFilter,ABC- classmethod end3s()
3’ end coordinates.
- classmethod end5s()
5’ end coordinates.
- class seismicrna.filter.tests.main_test.TestFilterSingle(*args, **kwargs)
Bases:
TestFilter,ABC- classmethod end3s()
3’ end coordinates.
- classmethod end5s()
5’ end coordinates.
- class seismicrna.filter.tests.main_test.TestFilterSingle1Sample1Batch(*args, **kwargs)
Bases:
TestFilterSingle,TestFilter1Sample,TestFilter1Batch- test_all_no_mut_min_ncov_read_7()
- test_dms_min_ncov_read_5()
- test_dms_min_ncov_read_6()
- test_drop_discontig()
- test_drop_read()
- test_drop_read_and_drop_read_file()
- test_drop_read_file()
- test_drop_read_files()
- test_mask_a()
- test_mask_c()
- test_mask_g()
- 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_files()
- test_mask_pos_min_ncov_read_5()
- test_mask_pos_min_ncov_read_6()
- test_mask_pos_multiple()
- test_mask_u()
- test_min_fcov_read_amplicons()
Two-PCR-amplicon scenario: filter reads that partially cover the useful region.
Positions 1 and 8 simulate 5’ and 3’ primers and are masked. Kept region after primer masking: positions 2-7 (6 nt, region.size=6).
Read5 (start=3, end=8) represents a read from an adjacent amplicon that begins inside amplicon A’s primer region. After masking position 8 (3’ primer), it covers positions 3-7 = 5/6 ≈ 0.83 → filtered.
All other reads start at position 1 or 2 and end at position 7 or 8, so after primer masking they each cover all 6 kept positions (positions 2-7) → fcov = 1.0 → kept.
- test_min_finfo_read_1()
- test_min_ncov_read_6()
- test_min_ncov_read_7()
- test_min_ncov_read_8()
- test_nomask()
- test_only_mut_ag_min_ninfo_pos_6()
- test_probe_dms()
- test_probe_dms_mask_a()
- test_probe_dms_mask_c()
- test_probe_dms_nomask_g()
- test_probe_dms_nomask_u()
- test_probe_etc()
- test_probe_etc_mask_g()
- test_probe_etc_mask_u()
- test_probe_etc_nomask_a()
- test_probe_etc_nomask_c()
- test_probe_shape()
- class seismicrna.filter.tests.main_test.TestSetMaskPolya(methodName='runTest')
Bases:
TestCase- test_dms_default()
- test_etc_default()
- test_explicit_value_none_default()
- test_explicit_value_overrides_default()
- test_explicit_zero_overrides_probe_default()
- test_none_default()
- test_shape_default()
- class seismicrna.filter.tests.main_test.TestSetMutGapParams(methodName='runTest')
Bases:
TestCase- test_auto_collisions_resolves_for_none_probe()
- test_dms_default_collisions()
- test_dms_default_gap()
- test_etc_default_collisions()
- test_etc_default_gap()
- test_explicit_collisions_drop_overrides_auto()
- test_explicit_collisions_merge_overrides_auto()
- test_explicit_gap_and_collisions()
- test_explicit_gap_overrides_default()
- test_explicit_zero_gap_overrides_default()
- test_none_default_collisions()
- test_none_default_gap()
- test_shape_default_collisions()
- test_shape_default_gap()
- seismicrna.filter.tests.main_test.extract_positions(dataset: FilterMutsDataset)
- seismicrna.filter.tests.main_test.extract_read_nums(dataset: FilterMutsDataset)