API Reference
Classes
Main classes provided by the package
- path_manager.ProjectPaths
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Manage project paths dynamically
Functions
Utility functions
- collect_bio_layer.collect_hipathia_pathway()
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Collecting HiPathia pathway information for the given species and export into given data folder.
- collect_bio_layer.create_pbk_matrix_hipathia_signaling()
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Exporting pathway and circuit dataset. The exported data gene vs pathway/circuit. It shows the connection details of each pathway-gene and circuit-gene pairs.
- collect_bio_layer.remove_disease_pathways()
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Removing disease-associated pathways from collected data. The data, by default, is collecting from HiPathia package. The raw data (input_pathway) is a list of pathway name and ID pairs.
- default_pbk_hipathia.convert_custom_list_into_list()
- default_pbk_hipathia.main()
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The entry point of collecting and exporting signaling pathways/circuits matrix
- default_pbk_hipathia.process_default_pbk()
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The main script that collects and export the signaling pathway/circut matrix.
- package_env_manager.check_env_line_exist()
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Checking the PYTHON and R environment information in .env file
- package_env_manager.load_dependencies()
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Locate and parse the dependencies.yml file which contains
- py_collect_gene_entrezid.py_gene_from_hipathia()
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Calling helper R-script to collect gene from HiPathia package.
- py_collect_gene_entrezid.py_gene_id_entrez_converter()
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Calling helper R-script to collect gene from HiPathia package.
- run_dependency.main()
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The entry points of downloading dependency list
- run_dependency.run_dependency_installer()
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Execution the installation of the essential package which are
- run_dependency.setup_project_env()
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Generate .env file and defining the PYTHON and R environment.
- spn_config.setup_project()
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Initialize project directories
Constants
Module-level constants and data