Example #1
0
def load_singlecore(args):
    # create a new gemini loader and populate
    # the gemini db and files from the VCF
    gemini_loader = GeminiLoader(args)
    gemini_loader.store_resources()
    gemini_loader.store_version()
    gemini_loader.store_vcf_header()
    gemini_loader.populate_from_vcf()
    gemini_db.add_max_aaf(gemini_loader.c)

    if not args.skip_gene_tables and not args.test_mode:
        gemini_loader.update_gene_table()
    if not args.test_mode:
        gemini_loader.build_indices_and_disconnect()

    if not args.no_genotypes and not args.no_load_genotypes:
        gemini_loader.store_sample_gt_counts()
Example #2
0
def load_singlecore(args):
    # create a new gemini loader and populate
    # the gemini db and files from the VCF
    gemini_loader = GeminiLoader(args)
    gemini_loader.store_resources()
    gemini_loader.store_version()
    gemini_loader.store_vcf_header()
    gemini_loader.populate_from_vcf()
    gemini_db.add_max_aaf(gemini_loader.c)

    if not args.skip_gene_tables and not args.test_mode:
        gemini_loader.update_gene_table()
    if not args.test_mode:
        gemini_loader.build_indices_and_disconnect()

    if not args.no_genotypes and not args.no_load_genotypes:
        gemini_loader.store_sample_gt_counts()
Example #3
0
def finalize_merged_db(tmp_db, db):
    ts = time.time()
    st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
    print st, "indexing final database."

    main_conn = sqlite3.connect(tmp_db)
    main_conn.isolation_level = None
    main_curr = main_conn.cursor()
    main_curr.execute('PRAGMA synchronous = OFF')
    main_curr.execute('PRAGMA journal_mode=MEMORY')

    gemini_db.add_max_aaf(main_curr)
    gemini_db.create_indices(main_curr)

    main_conn.commit()
    main_curr.close()

    shutil.move(tmp_db, db)
Example #4
0
def finalize_merged_db(tmp_db, db):
    ts = time.time()
    st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
    print st, "indexing final database."

    main_conn = sqlite3.connect(tmp_db)
    main_conn.isolation_level = None
    main_curr = main_conn.cursor()
    main_curr.execute('PRAGMA synchronous = OFF')
    main_curr.execute('PRAGMA journal_mode=MEMORY')

    gemini_db.add_max_aaf(main_curr)
    gemini_db.create_indices(main_curr)

    main_conn.commit()
    main_curr.close()

    shutil.move(tmp_db, db)