seismicrna.core.batch.tests package
Submodules
- class seismicrna.core.batch.tests.accum_test.TestAccumulateBatches(methodName='runTest')
Bases:
TestCase- test_cluster_2_batches()
. = Match, ! = Mutation, ? = Ambiguous, _ = Not Covered
3468 ACGT C1 C2 -------------- 2 _!?! 0.1 0.9 4 .!.. 0.3 0.7 7 !!!_ 0.5 0.5 -------------- 0 !!._ 0.6 0.4 6 ?.._ 0.8 0.2
- test_mask_2_batches()
. = Match, ! = Mutation, ? = Ambiguous, _ = Not Covered
3468 ACGT ------ 2 _!?! 4 .!.. 7 !!!_ ------ 0 !!._ 6 ?.._
- test_relate_1_batch()
. = Match, ! = Mutation, ? = Ambiguous, _ = Not Covered
1234 ACGT ------ 0 _!?! 1 .!.. 2 !!!_ 3 !!._ 4 ?.._
- test_relate_2_batches()
. = Match, ! = Mutation, ? = Ambiguous, _ = Not Covered
1234 ACGT ------ 0 _!?! 1 .!.. 2 !!!_ ------ 0 !!._ 1 ?.._
- seismicrna.core.batch.tests.accum_test.get_batch_count_all_func(batches: list[RegionMutsBatch])
- class seismicrna.core.batch.tests.confusion_test.TestCalcBhAdjustedPvals(methodName='runTest')
Bases:
TestCase- test_2d_ndarray_per_column()
- test_against_reference_implementation()
- test_all_nan()
- test_invalid_pvalues_raise()
- test_monotonicity_enforcement()
- test_nan_propagates_and_valid_entries_computed()
- test_order_invariance()
- test_pandas_dataframe()
- test_pandas_series_preserves_index()
- test_single_value()
- test_sorted_input_hand_calc()
- test_unsorted_input_hand_calc()
- class seismicrna.core.batch.tests.confusion_test.TestCalcConfusionMatrix(methodName='runTest')
Bases:
TestCase- test_clusters()
Pos. Rd. 2579 0 ==== 2 A=C= 3 =G=T 5 .G=. 8 ..== 9 T-=.
- test_no_clusters()
Pos. Rd. 2579 0 ==== 2 A=C= 3 =G=T 5 .G=. 8 ..== 9 T-=.
- class seismicrna.core.batch.tests.confusion_test.TestCalcConfusionPhi(methodName='runTest')
Bases:
TestCase- test_dataframe()
- test_series()
- class seismicrna.core.batch.tests.confusion_test.TestCountIntersection(methodName='runTest')
Bases:
TestCase- test_0_overlap()
- test_count_intersect()
- test_empty()
- test_first_overlap()
- test_last_overlap()
- test_middle_overlap()
- class seismicrna.core.batch.tests.confusion_test.TestInitConfusionMatrix(methodName='runTest')
Bases:
TestCase- test_clusters()
- test_no_clusters()
- test_no_clusters_min_gap()
- seismicrna.core.batch.tests.confusion_test.bh_ref_adjusted(p)
Reference BH adjusted p-values using scipy, NaN-safe.
- class seismicrna.core.batch.tests.count_test.TestCalcCountPerPos(methodName='runTest')
Bases:
TestCase- test_average()
11 13 14 15 Read A C G T -------------------- 0 1 64 1 255 1 255 255 1 255 5 128 1 1 16 6 255 1 1 17 7 1 64 1 255 9 128 1 1 1 10 1 1 1 255 11 1 1 1 1 14 64 3 1 1 16 255 255 1 1
- test_clusters()
11 13 14 15 Read A C G T -------------------- 0 1 64 1 255 1 255 255 1 255 5 128 1 1 16 6 255 1 1 17 7 1 64 1 255 9 128 1 1 1 10 1 1 1 255 11 1 1 1 1 14 64 3 1 1 16 255 255 1 1
- class seismicrna.core.batch.tests.count_test.TestCalcCountPerRead(methodName='runTest')
Bases:
TestCase- test_average()
11 13 14 15 17 Read A C G T C ------------------------ 0 1 64 1 255 255 1 255 255 1 255 255 5 128 1 1 16 1 6 255 1 1 17 64 7 1 64 1 255 255 9 128 1 1 1 16 10 1 1 1 255 255 11 1 1 1 1 1 14 64 3 1 1 128 16 255 255 1 1 2
- class seismicrna.core.batch.tests.count_test.TestCalcCoverage(methodName='runTest')
Bases:
TestCase- test_0_positions()
- test_0_positions_weighted()
- test_1_position()
- test_1_segment()
1234567890123 - -- --- --- - --- ------- ------------- ------- --- - --- --- -- -
- test_1_segment_mask()
1234567890123 . .. --- ... - --- ....... ............. ....... ... - ... ... .. .
- test_1_segment_redundant()
1234567890123 ------- ------- ------- ------- -------
- test_1_segment_redundant_weighted()
1234567890123 C1 C2 ------- 0.6 0.2 ------- 0.5 0.3 ------- 0.9 0.8 ------- 0.4 1.0 ------- 0.1 0.7
- test_1_segment_weighted()
1234567890123 C1 C2 - 0.1 1.5 -- 0.2 1.4 --- 0.3 1.3 --- 0.4 1.2 - 0.5 1.1 --- 0.6 1.0 ------- 0.7 0.9 ------------- 0.8 0.8 ------- 0.9 0.7 --- 1.0 0.6 - 1.1 0.5 --- 1.2 0.4 --- 1.3 0.3 -- 1.4 0.2 - 1.5 0.1
- test_2_segments_mask()
01234567890123 [---] ][ [---] ][ [---] ][ [---] ][ [---] [===] ][ [===] ][ [===] ][ [===] ][ [===]
- test_2_segments_nomask()
1234567890123 ----- ===== ----- ===== ---- ==== - = ---- ==== ----- ==== ------ ==== ------------- =============
- class seismicrna.core.batch.tests.count_test.TestCalcRelsPerPos(methodName='runTest')
Bases:
TestCase- test_average()
11 13 14 15 Read A C G T -------------------- 0 1 64 1 255 1 255 255 1 255 5 128 1 1 16 6 255 1 1 17 7 1 64 1 255 9 128 1 1 1 10 1 1 1 255 11 1 1 1 1 14 64 3 1 1 16 255 255 1 1
- test_clusters()
11 13 14 15 Read A C G T -------------------- 0 1 64 1 255 1 255 255 1 255 5 128 1 1 16 6 255 1 1 17 7 1 64 1 255 9 128 1 1 1 10 1 1 1 255 11 1 1 1 1 14 64 3 1 1 16 255 255 1 1
- class seismicrna.core.batch.tests.count_test.TestCalcRelsPerRead(methodName='runTest')
Bases:
TestCase- test_average()
11 13 14 15 17 Read A C G T C ------------------------ 0 1 64 1 255 255 1 255 255 1 255 255 5 128 1 1 16 1 6 255 1 1 17 64 7 1 64 1 255 255 9 128 1 1 1 16 10 1 1 1 255 255 11 1 1 1 1 1 14 64 3 1 1 128 16 255 255 1 1 2
- class seismicrna.core.batch.tests.count_test.TestCountEndCoords(methodName='runTest')
Bases:
TestCase- test_length_0()
- test_length_1()
- test_length_2_diff()
- test_length_2_same()
- test_length_3_diff_weights()
- test_length_3_same_weights()
- test_length_3_same_weights_int()
- class seismicrna.core.batch.tests.ends_test.TestCountReadsSegments(methodName='runTest')
Bases:
TestCase- test_non_array()
- test_valid()
- test_wrong_dims()
- class seismicrna.core.batch.tests.ends_test.TestFindContiguousReads(methodName='runTest')
Bases:
TestCase- test_0_segments()
- test_1_segment()
- test_2_segments_mask()
- test_2_segments_nomask()
- class seismicrna.core.batch.tests.ends_test.TestFindReadEnd3s(methodName='runTest')
Bases:
TestCase- test_0_segments()
- test_1_segment_masked()
- test_1_segment_none_masked()
- test_2_segments_both_masked()
- test_2_segments_masked()
- test_2_segments_none_masked()
- class seismicrna.core.batch.tests.ends_test.TestFindReadEnd5s(methodName='runTest')
Bases:
TestCase- test_0_segments()
- test_1_segment_masked()
- test_1_segment_none_masked()
- test_2_segments_both_masked()
- test_2_segments_masked()
- test_2_segments_none_masked()
- class seismicrna.core.batch.tests.ends_test.TestMatchReadsSegments(methodName='runTest')
Bases:
TestCase- test_match()
- class seismicrna.core.batch.tests.ends_test.TestMergeReadEnds(methodName='runTest')
Bases:
TestCase- test_mismatch()
- test_valid()
- test_wrong_dims()
- class seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds(methodName='runTest')
Bases:
TestCase- test_0_segments()
- test_1_segment_mask()
- test_1_segment_nomask()
- test_2_segments_mask()
- test_2_segments_nomask()
- test_n_segments_contig()
- test_n_segments_discontig()
- class seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix(methodName='runTest')
Bases:
TestCase- test_full_reads_no_muts()
- test_full_reads_no_muts_some_masked()
- test_paired_reads_masked_segments()
- test_paired_reads_no_muts()
- test_partial_reads_muts()
- test_partial_reads_no_muts()
- test_partial_reads_no_muts_some_masked()
- class seismicrna.core.batch.tests.muts_test.TestInjectCloseMuts(methodName='runTest')
Bases:
TestCase- region = Region(r__full:1-5)
- test_all_zero_probs()
- test_empty_mut_probs()
- test_existing_mutation_not_duplicated()
- test_invalid_above_one()
- test_invalid_ndim()
- test_invalid_negative()
- test_masked_position_skipped()
- test_only_mutated_reads_injected()
- test_original_mutation_preserved()
- test_prob_one_injects_all()
- test_read_not_covering_skipped()
- test_window_of_two()
- class seismicrna.core.batch.tests.muts_test.TestMergeCloseMuts(methodName='runTest')
Bases:
TestCase- region = Region(r__full:1-5)
- test_min_gap_zero_keeps_all()
- test_no_mutations()
- test_non_pattern_relationships_preserved()
- test_reads_processed_independently()
- test_single_mutation_survives()
- test_three_muts_middle_is_artifact()
- test_two_muts_gap_equals_min_gap()
- test_two_muts_gap_exceeds_min_gap()
- test_two_muts_gap_less_than_min_gap()