get_gb_records

Pipeline to retrieve GenBank records using accessions stored in the MySQL database.

pdm_utils.pipelines.get_gb_records.copy_gb_data(ncbi_handle, acc_id_dict, records_path, file_type, verbose=False)

Save retrieved records to file.

pdm_utils.pipelines.get_gb_records.execute_get_gb_records(alchemist, file_type, folder_path=None, folder_name='20220119_gb_records', config=None, values=None, verbose=False, force=False, filters='', groups=[])

Executes the entirety of the get_gb_records pipeline

Parameters

  • alchemist (AlchemyHandler) – A connected and fully build AlchemyHandler object.

  • folder_path (Path) – Path to a valid dir for new dir creation.

  • folder_name (str) – A name for the export folder.

  • file_type (str) – File type to be exported.

  • config (ConfigParser) – ConfigParser object containing NCBI credentials.

  • force (bool) – A boolean to toggle aggresive building of directories.

  • values (list[str]) – List of values to filter database results.

  • verbose (bool) – A boolean value to toggle progress print statemtns.

  • filters – A List of lists with filter value,grouped by ORs.

  • groups (list[str]) – A list of supported MySQL column names to goup by.

pdm_utils.pipelines.get_gb_records.main(unparsed_args_list)

Run main get_gb_records pipeline.

pdm_utils.pipelines.get_gb_records.parse_args(unparsed_args_list)

Parses export_db arguments and stores them with an argparse object.

Parameters

unparsed_args_list (list[str]) – Input a list of command line args.

Returns

ArgParse module parsed args.