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Getting SNP list from PredictDB database
import sqlite3
def get_snp_list(db_file, out_file):
'''
Queries a PredictDB sqlite database and creates a tab-delimited file with fields
rsid number, ref_allele, eff_allele.
db_file: path to the database file
out_file: name of the output file
'''
conn = sqlite3.connect(db_file)
with open(out_file, 'w') as snp_file:
snp_file.write('\t'.join(['rsid', 'ref_allele', 'eff_allele']) + '\n')
for row in conn.execute("SELECT DISTINCT rsid, ref_allele, eff_allele FROM weights"):
snp_file.write('\t'.join(row) + '\n')
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