15.1.1.6.1.2. cobra.test.test_flux_analysis
¶
15.1.1.6.1.2.1. Module Contents¶
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cobra.test.test_flux_analysis.
construct_ll_test_model
()¶
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cobra.test.test_flux_analysis.
ll_test_model
(request)¶
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cobra.test.test_flux_analysis.
construct_room_model
()¶
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cobra.test.test_flux_analysis.
construct_room_solution
()¶
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cobra.test.test_flux_analysis.
construct_geometric_fba_model
()¶
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cobra.test.test_flux_analysis.
captured_output
()¶ A context manager to test the IO summary methods.
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class
cobra.test.test_flux_analysis.
TestCobraFluxAnalysis
¶ Test the simulation functions in cobra.flux_analysis.
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test_pfba_benchmark
(large_model, benchmark, solver)¶
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test_pfba
(model, solver)¶
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test_geometric_fba_benchmark
(model, benchmark, solver)¶
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test_geometric_fba
(solver)¶
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test_single_gene_deletion_fba_benchmark
(model, benchmark, solver)¶
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test_single_gene_deletion_fba
(model, solver)¶
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test_single_gene_deletion_moma_benchmark
(model, benchmark, solver)¶
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test_single_gene_deletion_linear_moma_benchmark
(model, benchmark, solver)¶
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test_moma_sanity
(model, solver)¶ Test optimization criterion and optimality.
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test_single_gene_deletion_moma
(model, solver)¶
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test_single_gene_deletion_moma_reference
(model, solver)¶
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test_linear_moma_sanity
(model, solver)¶ Test optimization criterion and optimality.
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test_single_gene_deletion_linear_moma
(model, solver)¶
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test_single_gene_deletion_benchmark
(model, benchmark, solver)¶
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test_single_gene_deletion_room_benchmark
(model, benchmark, solver)¶
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test_single_gene_deletion_linear_room_benchmark
(model, benchmark, solver)¶
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test_room_sanity
(model, solver)¶
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test_linear_room_sanity
(model, solver)¶
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test_single_reaction_deletion_room
(solver)¶
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test_single_reaction_deletion_room_linear
(solver)¶
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test_single_reaction_deletion
(model, solver)¶
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compare_matrices
(matrix1, matrix2, places=3)¶
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test_double_gene_deletion_benchmark
(large_model, benchmark)¶
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test_double_gene_deletion
(model)¶
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test_double_reaction_deletion
(model)¶
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test_double_reaction_deletion_benchmark
(large_model, benchmark)¶
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test_flux_variability_benchmark
(large_model, benchmark, solver)¶
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test_flux_variability_loopless_benchmark
(model, benchmark, solver)¶
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test_pfba_flux_variability
(model, pfba_fva_results, fva_results, solver)¶
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test_flux_variability
(model, fva_results, solver)¶
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test_flux_variability_loopless
(model, solver)¶
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test_fva_data_frame
(model)¶
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test_fva_infeasible
(model)¶
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test_fva_minimization
(model)¶
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test_find_blocked_reactions_solver_none
(model)¶
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test_essential_genes
(model)¶
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test_essential_reactions
(model)¶
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test_find_blocked_reactions
(model, solver)¶
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test_loopless_benchmark_before
(benchmark)¶
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test_loopless_benchmark_after
(benchmark)¶
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test_loopless_solution
(ll_test_model)¶
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test_loopless_solution_fluxes
(model)¶
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test_add_loopless
(ll_test_model)¶
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test_gapfilling
(salmonella)¶
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check_line
(output, expected_entries, pattern=compile)¶ Ensure each expected entry is in the output.
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check_in_line
(output, expected_entries, pattern=compile)¶ Ensure each expected entry is contained in the output.
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test_model_summary_previous_solution
(model, opt_solver, names)¶
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test_model_summary
(model, opt_solver, names)¶
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test_model_summary_with_fva
(model, opt_solver, fraction)¶
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test_metabolite_summary_previous_solution
(model, opt_solver, met)¶
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test_metabolite_summary
(model, opt_solver, met, names)¶
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test_metabolite_summary_with_fva
(model, opt_solver, fraction, met)¶
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class
cobra.test.test_flux_analysis.
TestCobraFluxSampling
¶ Tests and benchmark flux sampling.
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test_single_achr
(model)¶
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test_single_optgp
(model)¶
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test_multi_optgp
(model)¶
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test_wrong_method
(model)¶
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test_validate_wrong_sample
(model)¶
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test_fixed_seed
(model)¶
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test_equality_constraint
(model)¶
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test_inequality_constraint
(model)¶
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setup_class
()¶
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test_achr_init_benchmark
(model, benchmark)¶
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test_optgp_init_benchmark
(model, benchmark)¶
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test_sampling
()¶
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test_achr_sample_benchmark
(benchmark)¶
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test_optgp_sample_benchmark
(benchmark)¶
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test_batch_sampling
()¶
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test_variables_samples
()¶
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test_inhomogeneous_sanity
(model)¶ Test whether inhomogeneous sampling gives approximately the same standard deviation as a homogeneous version.
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test_reproject
()¶
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test_complicated_model
()¶ Difficult model since the online mean calculation is numerically unstable so many samples weakly violate the equality constraints.
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test_single_point_space
(model)¶ Model where constraints reduce the sampling space to one point.
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