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)