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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,2 @@ | ||
| 1.3.0 | ||
| VDB_v5.2 | ||
| 1.4.0b | ||
| VDB_v6 |
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data/MicrobeAnnotator_KEGG/01.KEGG_DB/00.KEGG_Data_Scrapper.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,165 @@ | ||
| from bs4 import BeautifulSoup | ||
| import pandas as pd | ||
| import re | ||
| import pickle | ||
| import ast | ||
| import requests | ||
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| """ Script to download and parse KEGG information and store it in data """ | ||
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| def download_kegg_modules(module_name_file, chrome_driver): | ||
| module_ids =[] | ||
| module_names = {} | ||
| module_components_raw = {} | ||
| # Parse module names | ||
| with open(module_name_file) as module_input: | ||
| for line in module_input: | ||
| line = line.strip().split("\t") | ||
| module_ids.append(line[0]) | ||
| module_names[line[0]] = line[1] | ||
| # Access KEGG and download module information | ||
| for identifier in module_ids: | ||
| url = "https://www.kegg.jp/kegg-bin/show_module?" + identifier | ||
| site_request = requests.get(url) | ||
| soup = BeautifulSoup(site_request.text, "html.parser") | ||
| module_definition = "" | ||
| module_definition_bool = False | ||
| definition = soup.find(class_ = 'definition') | ||
| for line in (definition.text).splitlines(): | ||
| if line.strip() == "": | ||
| continue | ||
| elif module_definition_bool == True: | ||
| module_definition = line.strip() | ||
| module_definition_bool = False | ||
| elif line.strip() == 'Definition': | ||
| module_definition_bool = True | ||
| print(module_definition) | ||
| module_components_raw[identifier] = module_definition | ||
| return module_components_raw | ||
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| def parse_regular_module_dictionary(bifurcating_list_file, structural_list_file, module_components_raw): | ||
| bifurcating_list = [] | ||
| structural_list = [] | ||
| # Populate bifurcating and structural lists | ||
| with open(bifurcating_list_file, 'r') as bif_list: | ||
| for line in bif_list: | ||
| bifurcating_list.append(line.strip()) | ||
| with open(structural_list_file, 'r') as bif_list: | ||
| for line in bif_list: | ||
| structural_list.append(line.strip()) | ||
| # Parse raw module information | ||
| module_steps_parsed = {} | ||
| for key, values in module_components_raw.items(): | ||
| values = values.replace(" --", "") | ||
| values = values.replace("-- ", "") | ||
| if key in bifurcating_list or key in structural_list: | ||
| continue | ||
| else: | ||
| module = [] | ||
| parenthesis_count = 0 | ||
| for character in values: | ||
| if character == "(": | ||
| parenthesis_count += 1 | ||
| module.append(character) | ||
| elif character == " ": | ||
| if parenthesis_count == 0: | ||
| module.append(character) | ||
| else: | ||
| module.append("_") | ||
| elif character == ")": | ||
| parenthesis_count -= 1 | ||
| module.append(character) | ||
| else: | ||
| module.append(character) | ||
| steps = ''.join(module).split() | ||
| module_steps_parsed[key] = steps | ||
| # Remove modules depending on other modules | ||
| temporal_dictionary = module_steps_parsed.copy() | ||
| for key, values in temporal_dictionary.items(): | ||
| for value in values: | ||
| if re.search(r'M[0-9]{5}', value) is not None: | ||
| del module_steps_parsed[key] | ||
| break | ||
| return module_steps_parsed | ||
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| def create_final_regular_dictionary(module_steps_parsed, module_components_raw, outfile): | ||
| final_regular_dict = {} | ||
| # Parse module steps and export them into a text file | ||
| with open(outfile, 'w') as output: | ||
| for key, value in module_steps_parsed.items(): | ||
| output.write("{}\n".format(key)) | ||
| output.write("{}\n".format(module_components_raw[key])) | ||
| output.write("{}\n".format(value)) | ||
| output.write("{}\n".format("==")) | ||
| final_regular_dict[key] = {} | ||
| step_number = 0 | ||
| for step in value: | ||
| step_number += 1 | ||
| count = 0 | ||
| options = 0 | ||
| temp_string = "" | ||
| for char in step: | ||
| if char == "(": | ||
| count += 1 | ||
| options += 1 | ||
| if len(temp_string) > 1 and temp_string[-1] == "-": | ||
| temp_string += "%" | ||
| elif char == ")": | ||
| count -= 1 | ||
| if count >= 1: | ||
| temp_string += char | ||
| else: | ||
| continue | ||
| elif char == ",": | ||
| if count >= 2: | ||
| temp_string += char | ||
| print(step) | ||
| else: | ||
| temp_string += " " | ||
| else: | ||
| temp_string += char | ||
| if options >= 2: | ||
| temp_string = temp_string.replace(")_", "_") | ||
| if re.search('%.*\)', temp_string) is None: | ||
| temp_string = temp_string.replace(")", "") | ||
| temp_string = "".join(temp_string.rsplit("__", 1)) | ||
| temp_string = temp_string.split() | ||
| if isinstance(temp_string, str): | ||
| temp_string = temp_string.split() | ||
| temp_string = sorted(temp_string, key=len) | ||
| final_regular_dict[key][step_number] = temp_string | ||
| output.write("{}\n".format(temp_string)) | ||
| output.write("{}\n".format("++++++++++++++++++")) | ||
| return final_regular_dict | ||
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| def export_module_dictionary(dictionary, location): | ||
| pickle_out = open(location,"wb") | ||
| pickle.dump(dictionary, pickle_out) | ||
| pickle_out.close() | ||
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| def transform_module_dictionaries(bifurcating_data, structural_data, output_bifur, output_struct): | ||
| bifurcating_dictionary = ast.literal_eval(open(bifurcating_data).read()) | ||
| export_module_dictionary(bifurcating_dictionary, output_bifur) | ||
| structural_dictionary = ast.literal_eval(open(structural_data).read()) | ||
| export_module_dictionary(structural_dictionary, output_struct) | ||
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| # Execute parsing functions | ||
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| module_components_raw = download_kegg_modules("00.Module_Names.txt", 'chromedriver') | ||
| module_steps_parsed = parse_regular_module_dictionary("01.Bifurcating_List.txt", | ||
| "02.Structural_List.txt", module_components_raw) | ||
| final_regular_dict = create_final_regular_dictionary(module_steps_parsed, module_components_raw, "05.Modules_Parsed.txt") | ||
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| export_module_dictionary(final_regular_dict, "../01.KEGG_Regular_Module_Information.pickle") | ||
| transform_module_dictionaries("03.Bifurcating_Modules.dict", | ||
| "04.Structural_Modules.dict", | ||
| "../02.KEGG_Bifurcating_Module_Information.pickle", | ||
| "../03.KEGG_Structural_Module_Information.pickle") |
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