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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