spras

• spras package
  • Subpackages
    • spras.analysis package
      • Submodules
      • spras.analysis.cytoscape module
      • spras.analysis.ml module
      • spras.analysis.summary module
      • Module contents
    • spras.config package
      • Submodules
      • spras.config.config module
      • spras.config.schema module
      • spras.config.util module
      • Module contents
  • Submodules
  • spras.allpairs module
    • AllPairs
      • AllPairs.dois
      • AllPairs.generate_inputs()
      • AllPairs.parse_output()
      • AllPairs.required_inputs
      • AllPairs.run()
  • spras.btb module
    • BowTieBuilder
      • BowTieBuilder.dois
      • BowTieBuilder.generate_inputs()
      • BowTieBuilder.parse_output()
      • BowTieBuilder.required_inputs
      • BowTieBuilder.run()
  • spras.containers module
    • ContainerError
      • ContainerError.error_code
      • ContainerError.stderr
      • ContainerError.stdout
      • ContainerError.streams_contain()
    • convert_docker_path()
    • download_gcs()
    • env_to_items()
    • prepare_dsub_cmd()
    • prepare_path_docker()
    • prepare_volume()
    • run_container()
    • run_container_and_log()
    • run_container_docker()
    • run_container_dsub()
    • run_container_singularity()
    • upload_gcs()
  • spras.dataset module
    • Dataset
      • Dataset.NODE_ID
      • Dataset.contains_node_columns()
      • Dataset.from_file()
      • Dataset.get_interactome()
      • Dataset.get_node_columns()
      • Dataset.get_other_files()
      • Dataset.load_files_from_dict()
      • Dataset.to_file()
      • Dataset.warning_threshold
  • spras.domino module
    • DOMINO
      • DOMINO.dois
      • DOMINO.generate_inputs()
      • DOMINO.parse_output()
      • DOMINO.required_inputs
      • DOMINO.run()
    • DominoParams
      • DominoParams.model_config
      • DominoParams.module_threshold
      • DominoParams.slice_threshold
    • post_domino_id_transform()
    • pre_domino_id_transform()
  • spras.evaluation module
    • Evaluation
      • Evaluation.NODE_ID
      • Evaluation.datasets
      • Evaluation.directed_edge_table
      • Evaluation.edge_dummy_function()
      • Evaluation.edge_frequency_node_ensemble()
      • Evaluation.from_file()
      • Evaluation.label
      • Evaluation.merge_gold_standard_input()
      • Evaluation.mixed_edge_table
      • Evaluation.node_precision_and_recall()
      • Evaluation.node_table
      • Evaluation.pca_chosen_pathway()
      • Evaluation.precision_and_recall_pca_chosen_pathway()
      • Evaluation.precision_and_recall_per_pathway()
      • Evaluation.precision_recall_curve_node_ensemble()
      • Evaluation.to_file()
      • Evaluation.undirected_edge_table
      • Evaluation.visualize_precision_and_recall_plot()
    • GoldStandardDict
      • GoldStandardDict.data_dir
      • GoldStandardDict.dataset_labels
      • GoldStandardDict.edge_files
      • GoldStandardDict.label
      • GoldStandardDict.node_files
  • spras.interactome module
    • add_constant()
    • add_directionality_constant()
    • convert_directed_to_undirected()
    • convert_undirected_to_directed()
    • has_direction()
    • reinsert_direction_col_directed()
    • reinsert_direction_col_mixed()
    • reinsert_direction_col_undirected()
    • sort_and_deduplicate_undirected()
  • spras.logging module
    • indent()
  • spras.meo module
    • MEO
      • MEO.dois
      • MEO.generate_inputs()
      • MEO.parse_output()
      • MEO.required_inputs
      • MEO.run()
    • MEOParams
      • MEOParams.local_search
      • MEOParams.max_path_length
      • MEOParams.model_config
      • MEOParams.rand_restarts
    • write_properties()
  • spras.mincostflow module
    • MinCostFlow
      • MinCostFlow.dois
      • MinCostFlow.generate_inputs()
      • MinCostFlow.parse_output()
      • MinCostFlow.required_inputs
      • MinCostFlow.run()
    • MinCostFlowParams
      • MinCostFlowParams.capacity
      • MinCostFlowParams.flow
      • MinCostFlowParams.model_config
  • spras.omicsintegrator1 module
    • DummyMode
      • DummyMode.all
      • DummyMode.file
      • DummyMode.others
      • DummyMode.terminals
    • OmicsIntegrator1
      • OmicsIntegrator1.dois
      • OmicsIntegrator1.generate_inputs()
      • OmicsIntegrator1.parse_output()
      • OmicsIntegrator1.required_inputs
      • OmicsIntegrator1.run()
    • OmicsIntegrator1Params
      • OmicsIntegrator1Params.b
      • OmicsIntegrator1Params.d
      • OmicsIntegrator1Params.dummy_mode
      • OmicsIntegrator1Params.exclude_terms
      • OmicsIntegrator1Params.g
      • OmicsIntegrator1Params.model_config
      • OmicsIntegrator1Params.mu
      • OmicsIntegrator1Params.mu_squared
      • OmicsIntegrator1Params.noise
      • OmicsIntegrator1Params.noisy_edges
      • OmicsIntegrator1Params.r
      • OmicsIntegrator1Params.random_terminals
      • OmicsIntegrator1Params.seed
      • OmicsIntegrator1Params.shuffled_prizes
      • OmicsIntegrator1Params.w
    • write_conf()
  • spras.omicsintegrator2 module
    • DummyMode
      • DummyMode.all
      • DummyMode.others
      • DummyMode.terminals
    • OmicsIntegrator2
      • OmicsIntegrator2.dois
      • OmicsIntegrator2.generate_inputs()
      • OmicsIntegrator2.parse_output()
      • OmicsIntegrator2.required_inputs
      • OmicsIntegrator2.run()
    • OmicsIntegrator2Params
      • OmicsIntegrator2Params.b
      • OmicsIntegrator2Params.dummy_mode
      • OmicsIntegrator2Params.g
      • OmicsIntegrator2Params.model_config
      • OmicsIntegrator2Params.noise
      • OmicsIntegrator2Params.noisy_edges
      • OmicsIntegrator2Params.random_terminals
      • OmicsIntegrator2Params.seed
      • OmicsIntegrator2Params.w
  • spras.pathlinker module
    • PathLinker
      • PathLinker.dois
      • PathLinker.generate_inputs()
      • PathLinker.parse_output()
      • PathLinker.required_inputs
      • PathLinker.run()
    • PathLinkerParams
      • PathLinkerParams.k
      • PathLinkerParams.model_config
  • spras.prm module
    • PRM
      • PRM.dois
      • PRM.generate_inputs()
      • PRM.get_params_generic()
      • PRM.parse_output()
      • PRM.required_inputs
      • PRM.run()
      • PRM.run_typeless()
      • PRM.validate_required_inputs()
      • PRM.validate_required_run_args()
  • spras.responsenet module
    • ResponseNet
      • ResponseNet.dois
      • ResponseNet.generate_inputs()
      • ResponseNet.parse_output()
      • ResponseNet.required_inputs
      • ResponseNet.run()
    • ResponseNetParams
      • ResponseNetParams.gamma
      • ResponseNetParams.model_config
  • spras.runner module
    • get_algorithm()
    • get_required_inputs()
    • merge_input()
    • parse_output()
    • prepare_inputs()
    • run()
  • spras.rwr module
    • RWR
      • RWR.dois
      • RWR.generate_inputs()
      • RWR.parse_output()
      • RWR.required_inputs
      • RWR.run()
    • RWRParams
      • RWRParams.alpha
      • RWRParams.model_config
      • RWRParams.threshold
  • spras.strwr module
    • ST_RWR
      • ST_RWR.dois
      • ST_RWR.generate_inputs()
      • ST_RWR.parse_output()
      • ST_RWR.required_inputs
      • ST_RWR.run()
    • ST_RWRParams
      • ST_RWRParams.alpha
      • ST_RWRParams.model_config
      • ST_RWRParams.threshold
  • spras.util module
    • NpHashEncoder
      • NpHashEncoder.default()
    • add_rank_column()
    • duplicate_edges()
    • hash_filename()
    • hash_params_sha1_base32()
    • make_required_dirs()
    • raw_pathway_df()
  • Module contents