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rdf.py
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import time
from selenium import webdriver
from selenium.webdriver.common.keys import Keys
import traceback
import pandas as pd
import glob
import shutil
import os
import datetime
from webdriver_manager.chrome import ChromeDriverManager
from selenium.webdriver.chrome.service import Service as ChromeService
def get_new_gene_file():
d_today = str(datetime.date.today())
current_download_url = "https://pubchem.ncbi.nlm.nih.gov/#query=covid-19&tab=gene"
options = webdriver.ChromeOptions()
# デフォルトダウンロードフォルダを変更する
options.add_experimental_option(
"prefs", {"download.default_directory": "datalist_csv"}
)
# 自動テストソフトウェアによって制御されていますというメッセージを非表示にする
options.add_experimental_option("excludeSwitches", ["enable-automation"])
# 拡張機能の自動更新をさせない（アプリ側の自動アップデートとドライバーの互換性によるエラーを回避）
options.add_experimental_option("useAutomationExtension", False)
# ヘッドレスモードの設定
options.add_argument("--headless")
driver = webdriver.Chrome(ChromeDriverManager().install(), options=options)
try:
os.mkdir("datalist_csv")
except:
pass
try:
print("START: Get new gene list.")
driver.implicitly_wait(5)
driver.get(current_download_url)
driver.find_element_by_tag_name("body").click()
for i in range(5):
driver.find_element_by_tag_name("body").send_keys(Keys.PAGE_DOWN)
time.sleep(3)
# JavaScrptの実行
# downloadのdropdownをクリックして開く
elements = driver.find_elements_by_xpath('//*[@id="Download"]/div/div[2]')
elements[0].click()
# csvを選択してgenelistをダウンロード
elements = driver.find_elements_by_xpath(
'//*[@id="collection-results-container"]/div/aside/div/div/div/div/div[1]/div/div[2]/div/div[2]/div[1]/div[1]/div[1]/a/span'
)
elements[0].click()
time.sleep(5)
# https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?infmt=json&outfmt=csv&query={%22download%22:%22*%22,%22collection%22:%22compound%22,%22where%22:{%22ands%22:[{%22*%22:%22covid-19%22}]},%22order%22:[%22relevancescore,desc%22],%22start%22:1,%22limit%22:10000000,%22downloadfilename%22:%22PubChem_compound_text_covid-19%22}
os.rename(
"./datalist_csv/PubChem_gene_text_covid-19.csv",
"./datalist_csv/PubChem_gene_text_covid-19_" + d_today + ".csv",
)
print("DONE: Get new gene list.")
except:
traceback.print_exc()
finally:
driver.quit()
def get_new_gene_list():
d_today = str(datetime.date.today())
now_genelist = {
"date": d_today,
"file_dir": "./datalist_csv/PubChem_gene_text_covid-19_" + d_today + ".csv",
"csv": [],
}
now_genelist["csv"] = pd.read_csv(now_genelist["file_dir"])
# current_genelist['csv'] = pd.read_csv(current_genelist['file_dir'])
# gene_list = list(
# set(now_genelist['csv']['geneid']) - set(current_genelist['csv']['geneid']))
gene_list = now_genelist["csv"]["geneid"]
return gene_list
def scrape(gene_list):
"""
Scrate every gene resource in PubChem web page and save data/gene/ directory
"""
print("START: Scrape PubChem resources.")
# 任意のディレクトリを指定
download_directory = "data/gene/"
download_url = "https://pubchem.ncbi.nlm.nih.gov/gene/"
# gene_csv = pd.read_csv("./datalist_/Pubchem_gene_text_covid-19.csv")
try:
os.makedirs("data/gene")
except:
pass
for i in range(len(gene_list)):
print("get new gene ", gene_list[i])
current_download_directory = download_directory + str(gene_list[i])
current_download_url = download_url + str(gene_list[i])
options = webdriver.ChromeOptions()
# デフォルトダウンロードフォルダを変更する
options.add_experimental_option(
"prefs", {"download.default_directory": current_download_directory}
)
# 自動テストソフトウェアによって制御されていますというメッセージを非表示にする
options.add_experimental_option("excludeSwitches", ["enable-automation"])
# 拡張機能の自動更新をさせない（アプリ側の自動アップデートとドライバーの互換性によるエラーを回避）
options.add_experimental_option("useAutomationExtension", False)
# ヘッドレスモードの設定
# options.add_argument("--headless")
driver = webdriver.Chrome(ChromeDriverManager().install(), options=options)
try:
os.mkdir(current_download_directory)
except:
pass
try:
driver.implicitly_wait(5)
driver.get(current_download_url)
driver.find_element_by_tag_name("body").click()
for i in range(100):
driver.find_element_by_tag_name("body").send_keys(Keys.PAGE_DOWN)
time.sleep(4)
# JavaScriptの実行
# ダウンロードボタンを押すために邪魔となっているsticky-barをremoveする
driver.execute_script(
"document.getElementsByClassName('sticky-bar')[0].remove();"
)
elements = driver.find_elements_by_xpath(
"//button[@data-action='popup-menu-open']"
)
for e in elements:
e.click()
save_button = e.find_element_by_xpath("//a[text()='CSV']")
print(save_button)
print(dir(save_button))
if save_button:
save_button.click()
time.sleep(2)
except:
pass
finally:
time.sleep(5)
driver.quit()
if i % 100 == 0:
print(str(i) + "/" + str(len(gene_list)) + " Done.")
print("Done: Scrape PubChem resources.")
def mkdir():
"""
data/gene/のファイルを分類してdata/dir/に入れていく
"""
mkdir_dir = "data/dir/"
directry = "data/gene"
mkdir_tuple = (
"pdb",
"bioactivity_gene",
"drugbank",
"chembldrug",
"gtopdb",
"bioassay",
"gene_disease",
"geneinter",
"dgidb",
"ctdchemicalgene",
"pathwayreaction",
"pathwaygene",
"rhea",
)
for f in mkdir_tuple:
try:
os.makedirs(mkdir_dir + f)
except:
print("File exists: " + mkdir_dir + f)
# 任意の親ディレクトリに各ファイル用のディレクトリを作成
# pdbディレクトリの作成
l = glob.glob(directry + "/**/*_pdb*.csv", recursive=True)
for i in range(len(l)):
new_path = shutil.copy(l[i], mkdir_dir + "pdb")
# tested compounds (bioactivity gene)ディレクトリの作成
l_bio_gene = glob.glob(directry + "/**/*_bioactivity_gene*.csv", recursive=True)
for i in range(len(l_bio_gene)):
new_path_bio_gene = shutil.copy(l_bio_gene[i], mkdir_dir + "bioactivity_gene")
# drugbank drugsディレクトリの作成
l_drugbank = glob.glob(directry + "/**/*_drugbank*.csv", recursive=True)
for i in range(len(l_drugbank)):
new_path_drugbank = shutil.copy(l_drugbank[i], mkdir_dir + "drugbank")
# chembl drugディレクトリの作成
l_chembl = glob.glob(directry + "/**/*_chembldrugtargets*.csv", recursive=True)
for i in range(len(l_chembl)):
new_path_chembl = shutil.copy(l_chembl[i], mkdir_dir + "chembldrug")
# guide to pharmacology ligands ディレクトリ
l_gtopdb = glob.glob(directry + "/**/*_gtopdb*.csv", recursive=True)
for i in range(len(l_gtopdb)):
new_path_gtopdb = shutil.copy(l_gtopdb[i], mkdir_dir + "gtopdb")
# bioassay ディレクトリ
l_bioassay = glob.glob(directry + "/**/*_bioassay*.csv", recursive=True)
for i in range(len(l_bioassay)):
new_path_bioassay = shutil.copy(l_bioassay[i], mkdir_dir + "bioassay")
# ctd gene-disease ディレクトリ
l_gene_disease = glob.glob(directry + "/**/*_ctd_gene_disease*.csv", recursive=True)
for i in range(len(l_gene_disease)):
new_path_gene_disease = shutil.copy(
l_gene_disease[i], mkdir_dir + "gene_disease"
)
# gene-gene interaction ディレクトリ
l_geneinter = glob.glob(directry + "/**/*_geneinteractions*.csv", recursive=True)
for i in range(len(l_geneinter)):
new_path_geneinter = shutil.copy(l_geneinter[i], mkdir_dir + "geneinter")
# drug-gene interaction ディレクトリ
l_dgidb = glob.glob(directry + "/**/*_dgidb*.csv", recursive=True)
for i in range(len(l_dgidb)):
new_path_dgidb = shutil.copy(l_dgidb[i], mkdir_dir + "dgidb")
# ctd chemical-gene interactions ディレクトリ
l_ctdchemicalgene = glob.glob(
directry + "/**/*_ctdchemicalgene*.csv", recursive=True
)
for i in range(len(l_ctdchemicalgene)):
new_path_ctdchemicalgene = shutil.copy(
l_ctdchemicalgene[i], mkdir_dir + "ctdchemicalgene"
)
# pathwayreaction ディレクトリ
l_pathwayreaction = glob.glob(
directry + "/**/*_pathwayreaction*.csv", recursive=True
)
for i in range(len(l_pathwayreaction)):
new_path_pathwayreaction = shutil.copy(
l_pathwayreaction[i], mkdir_dir + "pathwayreaction"
)
# pathwayディレクトリ
l_pathway = glob.glob(directry + "/**/*_pathway*.csv", recursive=True)
for i in range(len(l_pathway)):
new_path_pathway = shutil.copy(l_pathway[i], mkdir_dir + "pathwaygene")
# RHEAディレクトリ
l_rhea = glob.glob(directry + "/**/*_rhea*.csv", recursive=True)
for i in range(len(l_rhea)):
new_path_rhea = shutil.copy(l_rhea[i], mkdir_dir + "rhea")
if __name__ == "__main__":
# get_new_gene_file()
# gene_list = get_new_gene_list()
# scrape(gene_list)
mkdir()