def setUp(self): varFinder.loadDb(logLevel=100) # disable logging self.genes = [672, 675] # BRCA1 and BRCA2 entrez ids self.c_variant_del_text = "The variant c.3616delG is pathogenic." self.c_variant_del_found = varFinder.findVariantDescriptions( self.c_variant_del_text, []) self.c_variant_sub_text = "We found that the variant c.135C>T may do some stuff." self.c_variant_sub_found = varFinder.findVariantDescriptions( self.c_variant_sub_text, []) self.c_variant_sub_offset_text = "We found that the variant c.135-563C>T may do some stuff." self.c_variant_sub_offset_found = varFinder.findVariantDescriptions( c_variant_sub_offset_text, [])
def startup(paramDict): varFinder.loadDb() geneFinder.initData(exclMarkerTypes=["dnaSeq"])
def startup(paramDict): geneFinder.initData(exclMarkerTypes=["dnaSeq", "band"]) #varFinder.loadDb(loadSequences=False) varFinder.loadDb()