def get_pp2(self):
b = MyBrowser(head=False)
b.clinvar_missense_nav(self.gene)
total_missense = b.browser.find_by_xpath(
'//*[@id="_molConseq"]/li/ul/li[2]/span').value
total_missense = int(total_missense[1:][:-1])
benign_missense = b.browser.find_by_xpath(
'//*[@id="_Properties"]/li/ul/li[2]/span').value
benign_missense = int(benign_missense[1:][:-1])
likely_benign_missense = b.browser.find_by_xpath(
'//*[@id="_Properties"]/li/ul/li[3]/span').value
likely_benign_missense = int(likely_benign_missense[1:][:-1])
if (likely_benign_missense + benign_missense) / total_missense < 0.1:
return True
else:
return False
b = MyBrowser()
# gnomAD
b.gnomad_nav(variant.chr, variant.pos, variant.ref, variant.alt)
b.take_screenshot(screenshot_path, 'gnomAD.jpg', 350, 200, 1600, 900)
# dbNSFP
b.dbnsfp_nav(variant.chr, variant.pos, variant.ref, variant.alt)
b.take_screenshot(screenshot_path, 'dbNSFP.jpg', 270, 170, 670, 1000)
# GERP
b.gerp_nav(variant.chr, variant.pos, variant.ref, variant.alt)
b.take_screenshot(screenshot_path, 'GERP.jpg', 270, 170, 1170, 600)
## ClinVar missense
b.clinvar_missense_nav(variant.gene)
b.take_screenshot(screenshot_path, 'clinvar_missense.jpg', 5, 290, 193,
886)
## Unclick missense
b.browser.find_by_text('Missense').click()
## ClinVar P/LP
b.clinvar_path_nav(variant.gene)
b.take_screenshot(screenshot_path, 'clinvar_plp.jpg', 5, 290, 193, 886)
## ExAC
b.exac_nav(variant.gene)
b.take_screenshot(screenshot_path, 'exac.jpg', 36, 200, 1750, 500)
## OMIM
