def main(): "Everything starts here" if len(sys.argv) >= 2: if sys.argv[1] == "variants-list": vl1 = VariantsLister(sys.argv[2:]) return vl1.main() elif sys.argv[1] == "evidence-items-list": eil1 = EvidenceItemsLister(sys.argv[2:]) return eil1.main() elif sys.argv[1] == "action-items-web-view": web_view() elif sys.argv[1] == "tsv-create": tsv1 = TsvFileLister(sys.argv[2:]) return tsv1.main() else: return usage()
def create_invalid_eis_list(self): "Create the list of invalid evidence items" vl1 = VariantsLister(self.args) vl1.get_civic_genes() variant_ids = vl1.get_variant_ids() for variant_id in variant_ids: variant_detail = vl1.get_variant_details(variant_id) if "evidence_items" in variant_detail: evidence_items = variant_detail['evidence_items'] if self.args.doid: #If not valid, add to list of invalids self.check_doid(variant_id, variant_detail, evidence_items) if self.args.drug: #If drug doesn't exist, add to list of invalids self.check_drug_for_pre(variant_id, variant_detail,evidence_items) # if neither of the flags were specified, do both checks if not (self.args.doid or self.args.drug): self.check_doid(variant_id, variant_detail, evidence_items) self.check_drug_for_pre(variant_id, variant_detail,evidence_items)
def get_info_and_print(self): "Get variants and evidence items " vl1 = VariantsLister(self.args) vl1.get_civic_genes() variant_ids = vl1.get_variant_ids() file_name = 'ClinicalEvidenceSummary_'+time.strftime('%d%m%Y')+'.tsv' output = open(file_name,'w') header = self.make_header() output.write(header) for variant_id in variant_ids: variant_detail = vl1.get_variant_details(variant_id) if "evidence_items" in variant_detail: evidence_items = variant_detail['evidence_items'] for evidence_item in evidence_items: tsv_item = TsvEvidenceItmes(variant_detail, evidence_item) output.write(tsv_item.make_str_for_print()) output.close()
def main(): "Everything starts here" try: if len(sys.argv) >= 2: if sys.argv[1] == "variants-list": vl1 = VariantsLister(sys.argv[2:]) return vl1.main() elif sys.argv[1] == "evidence-items-list": eil1 = EvidenceItemsLister(sys.argv[2:]) return eil1.main() elif sys.argv[1] == "action-items-web-view": web_view() elif sys.argv[1] == "tsv-create": tsv1 = TsvFileLister(sys.argv[2:]) return tsv1.main() else: return usage() except KeyboardInterrupt: print ("Interrupted!") sys.exit(0)
def variants(): vl1 = VariantsLister(sys.argv[2:]) vl1.parse_args() vl1.create_filtered_variants_list() filtered_variant_details = vl1.get_filtered_variant_details() return render_template('variants.html', \ filtered_variant_details= filtered_variant_details)