spras

• spras package
  • Subpackages
    • spras.analysis package
      • Submodules
      • spras.analysis.cytoscape module
      • spras.analysis.ml module
      • spras.analysis.summary module
      • Module contents
  • Submodules
  • spras.allpairs module
    • AllPairs
      • AllPairs.dois
      • AllPairs.generate_inputs()
      • AllPairs.parse_output()
      • AllPairs.required_inputs
      • AllPairs.run()
  • spras.config module
  • spras.containers module
    • 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()
    • post_domino_id_transform()
    • pre_domino_id_transform()
  • spras.evaluation module
    • Evaluation
      • Evaluation.NODE_ID
      • Evaluation.edge_frequency_node_ensemble()
      • Evaluation.from_file()
      • Evaluation.load_files_from_dict()
      • Evaluation.merge_gold_standard_input()
      • Evaluation.node_precision_and_recall()
      • 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.visualize_precision_and_recall_plot()
  • 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()
  • spras.meo module
    • MEO
      • MEO.dois
      • MEO.generate_inputs()
      • MEO.parse_output()
      • MEO.required_inputs
      • MEO.run()
    • write_properties()
  • spras.mincostflow module
    • MinCostFlow
      • MinCostFlow.dois
      • MinCostFlow.generate_inputs()
      • MinCostFlow.parse_output()
      • MinCostFlow.required_inputs
      • MinCostFlow.run()
  • spras.omicsintegrator1 module
    • OmicsIntegrator1
      • OmicsIntegrator1.dois
      • OmicsIntegrator1.generate_inputs()
      • OmicsIntegrator1.parse_output()
      • OmicsIntegrator1.required_inputs
      • OmicsIntegrator1.run()
    • write_conf()
  • spras.omicsintegrator2 module
    • OmicsIntegrator2
      • OmicsIntegrator2.dois
      • OmicsIntegrator2.generate_inputs()
      • OmicsIntegrator2.parse_output()
      • OmicsIntegrator2.required_inputs
      • OmicsIntegrator2.run()
  • spras.pathlinker module
    • PathLinker
      • PathLinker.dois
      • PathLinker.generate_inputs()
      • PathLinker.parse_output()
      • PathLinker.required_inputs
      • PathLinker.run()
  • spras.prm module
    • PRM
      • PRM.dois
      • PRM.generate_inputs()
      • PRM.parse_output()
      • PRM.required_inputs
      • PRM.run()
      • PRM.validate_required_inputs()
  • spras.runner module
    • get_algorithm()
    • get_required_inputs()
    • merge_input()
    • parse_output()
    • prepare_inputs()
    • run()
  • 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