seismicrna.duplex.tests package
Submodules
- class seismicrna.duplex.tests.duplex_test.DuplexClusterProductTest(methodName='runTest')
Bases:
TestCaseA duplex of clustered sources is the cross-product of their clusters.
- setUp()
Hook method for setting up the test fixture before exercising it.
- tearDown()
Hook method for deconstructing the test fixture after testing it.
- test_average_source_stays_unclustered()
Combining two unclustered strands yields one average profile.
- test_cluster_product_with_no_data_partner()
A clustered strand duplexed with a data-less partner gives one fused profile per cluster of the clustered strand, each of which cofolds on its own reactivities.
- test_cross_product_count()
K1 x K2 clusters give K1*K2 fused profiles over the duplex.
- test_cross_product_folds()
Each fused cluster profile folds into its own duplex.
- test_cross_product_maps_source_clusters()
Combination n=(i,j) carries strand-1 cluster i on the 5’ side and strand-2 cluster j on the 3’ side (product order).
- test_fallback_table_without_a_best_k()
A clustered table whose cluster step found no best number of clusters (best_k = 0, its fallback) is duplexed using the one number of clusters it contains, rather than producing none.
- test_no_best_k_and_several_ks_is_an_error()
If several numbers of clusters are available and none is best, which to duplex is ambiguous, so it raises rather than guessing.
- test_propagates_parent_branch()
A parent (source) branch is carried into the duplex path.
- test_rejects_mismatched_parent_branches()
Two data sources on different branches cannot be duplexed.
- test_rejects_mismatched_probes()
Two data sources probed with different chemicals cannot be duplexed (the duplex folds with one energy method).
- class seismicrna.duplex.tests.duplex_test.DuplexEnergyMethodTest(methodName='runTest')
Bases:
TestCaseCofolding uses SHAPE flags directly (Deigan), DMS pseudo-energies (Cordero), and rejects any method RNAcofold cannot express.
- test_cordero_fit_is_per_strand()
Each strand’s Cordero pseudoenergies are fit independently, so one strand’s reactivities do not affect the other’s (a pooled fit would couple them through a shared scale factor).
- test_cordero_uses_pseudomus()
Cordero (DMS) feeds pseudo-mutation rates, not reactivities.
- test_deigan_uses_shape_flags()
Deigan feeds reactivities with the user’s slope/intercept.
- test_profile_rejects_unsupported()
- test_resolve_auto()
- test_resolve_passthrough()
- test_resolve_rejects_unsupported()
- class seismicrna.duplex.tests.duplex_test.DuplexPairingTest(methodName='runTest')
Bases:
TestCaseEvery way of choosing the 3’ strand contributes its own duplexes, so they compose rather than override one another.
- setUp()
Hook method for setting up the test fixture before exercising it.
- tearDown()
Hook method for deconstructing the test fixture after testing it.
- test_all_sources_compose()
Pairwise, –dimer, and a partner sequence all contribute at once; none of them suppresses the others.
- test_no_duplex_pair_leaves_partners()
–no-duplex-pair drops only the pairwise combinations.
- test_nothing_to_duplex()
With every source of pairs turned off, nothing is made.
- test_pairwise_is_the_default()
- test_rerunning_does_not_duplex_duplexes()
Running duplex again over a directory that already holds its own output makes the same duplexes, not chimeras of them: a duplex table among the inputs is not a strand of a new duplex.
- class seismicrna.duplex.tests.duplex_test.DuplexTest(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_duplex_dimer()
–dimer combines a table with itself into a homodimer.
- test_duplex_named_sequence_partner()
A (name, sequence) partner names the 3’ strand.
- test_duplex_sequence_partner()
A data-less partner sequence becomes the 3’ strand: the duplex loads, its cut is the 5’ strand’s length, and the partner’s positions carry no data.
- test_fold_duplex_is_graphable()
Folding a duplex produces a duplex structure (via RNAcofold) that pairs with the duplex profile as one entity.
- test_loads_via_api()
A duplex table loads like any position table and reconstructs the fused identity, the strand break, and its two sources.
- test_per_reference_region_override()
Per-reference overrides beat the global default in both directions, and a conflict is rejected.
- class seismicrna.duplex.tests.duplex_test.IterDuplexPairsTest(methodName='runTest')
Bases:
TestCaseDuplex candidates are grouped by branches (what make_duplex requires of two strands) and paired in a deterministic order.
- test_every_pair()
- test_groups_by_branches()
- test_groups_by_step_not_flattened_branches()
Tables from different steps do not pair, even on default branches: flattening the branches would drop every step and every empty branch name, making a filter table and a duplex table look alike, but make_duplex compares the branches themselves.
- test_one_table_makes_no_pair()
- test_order_independent()