kg_covid_19.transform_utils.drug_central package

Submodules

kg_covid_19.transform_utils.drug_central.drug_central module

class kg_covid_19.transform_utils.drug_central.drug_central.DrugCentralTransform(input_dir: str = None, output_dir: str = None)

Bases: kg_covid_19.transform_utils.transform.Transform

run(data_file: Optional[str] = None, species: str = 'Homo sapiens') → None

Method is called and performs needed transformations to process the Drug Central data, additional information on this data can be found in the comment at the top of this script

kg_covid_19.transform_utils.drug_central.drug_central.items_dict_to_protein_data_dict(items_dict: dict) → dict

Given a parsed line from parse_drug_central_line, split up pipe-separated entries for several related proteins and their names and TDL info into separate protein entries

Parameters

items_dict – dictionary of data from a line, output by parse_drug_central_line

Returns

a dict with information about each protein

kg_covid_19.transform_utils.drug_central.drug_central.parse_drug_central_line(this_line: str, header_items: List) → Dict

Methods processes a line of text from Drug Central.

Args:

this_line: A string containing a line of text. header_items: A list of header items.

Returns:

item_dict: A dictionary of header items and a processed Drug Central string.

Module contents

class kg_covid_19.transform_utils.drug_central.DrugCentralTransform(input_dir: str = None, output_dir: str = None)

Bases: kg_covid_19.transform_utils.transform.Transform

run(data_file: Optional[str] = None, species: str = 'Homo sapiens') → None

Method is called and performs needed transformations to process the Drug Central data, additional information on this data can be found in the comment at the top of this script