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
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
7 !!!_
0 !!._ 6 ?.._
- test_relate_1_batch()
. = Match ! = Mutation ? = Ambiguous _ = Not Covered
1234 ACGT
2 !!!_ 3 !!._ 4 ?.._
- seismicrna.core.batch.tests.accum_test.get_batch_count_all_func(batches: list[RegionMutsBatch])
- class seismicrna.core.batch.tests.count_test.TestCalcCountPerPos(methodName='runTest')
Bases:
TestCase
- class seismicrna.core.batch.tests.count_test.TestCalcCountPerRead(methodName='runTest')
Bases:
TestCase
- 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_redundant()
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- test_1_segment_redundant_weighted()
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- ——- 0.6 0.2
- ——- 0.5 0.3
——- 0.9 0.8
——- 0.4 1.0
——- 0.1 0.7
- test_1_segment_weighted()
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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()
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- test_2_segments_nomask()
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- class seismicrna.core.batch.tests.count_test.TestCalcRelsPerPos(methodName='runTest')
Bases:
TestCase
- class seismicrna.core.batch.tests.count_test.TestCalcRelsPerRead(methodName='runTest')
Bases:
TestCase
- class seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights(methodName='runTest')
Bases:
TestCase- test_0_reads()
- test_1_read()
- test_2_reads_1_uniq()
- test_2_reads_2_uniq()
- 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.TestCheckNoCoverageReads(methodName='runTest')
Bases:
TestCase- test_1_segment_all_covered()
- test_1_segment_none_covered()
- test_2_segments_all_covered()
- test_2_segments_half_covered()
- test_2_segments_none_covered()
- class seismicrna.core.batch.tests.ends_test.TestCountReadsSegments(methodName='runTest')
Bases:
TestCase- test_0_segments()
- test_non_array()
- test_valid()
- test_wrong_dims()
- class seismicrna.core.batch.tests.ends_test.TestFindContiguousReads(methodName='runTest')
Bases:
TestCase- test_1_segment()
- test_2_segments_mask()
- test_2_segments_nomask()
- class seismicrna.core.batch.tests.ends_test.TestFindReadEnd3s(methodName='runTest')
Bases:
TestCase- test_1_segment()
- test_2_segments_mask()
- test_2_segments_nomask()
- class seismicrna.core.batch.tests.ends_test.TestFindReadEnd5s(methodName='runTest')
Bases:
TestCase- test_1_segment()
- test_2_segments_mask()
- test_2_segments_nomask()
- class seismicrna.core.batch.tests.ends_test.TestMaskSegmentEnds(methodName='runTest')
Bases:
TestCase- test_mask()
- test_nomask()
- 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.TestMergeSegmentEnds(methodName='runTest')
Bases:
TestCase- test_mask()
- test_nomask()
- class seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds(methodName='runTest')
Bases:
TestCase- test_1_segment()
- test_2_segments_mask()
- test_2_segments_nomask()
- test_2_segments_unmask()
- 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()