Created
February 13, 2019 21:13
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Get all variants in CIViC for a specific entrez symbol
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import requests | |
entrez_symbol = 'BRAF' | |
gene_url = 'https://civicdb.org/api/genes/{}?identifier_type=entrez_symbol'.format(entrez_symbol) | |
gene_response = requests.get(gene_url) | |
gene_body = gene_response.json() | |
variant_details = [] | |
variants_with_evidence = [variant for variant in gene_body['variants'] if variant['evidence_items']['accepted_count'] > 0] | |
for variant in variants_with_evidence: | |
variant_detail_url = 'https://civicdb.org/api/variants/{}'.format(variant['id']) | |
variant_detail_response = requests.get(variant_detail_url) | |
variant_detail_body = variant_detail_response.json() | |
variant_details.append(variant_detail_body) | |
print('Retrieved {} variants for gene {}, the last of which is named {}.' | |
.format(len(variant_details), entrez_symbol, variant_details[-1]['name'])) |
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