Exemplo n.º 1
0
def load_singlecore(args):
    # create a new gemini loader and populate
    # the gemini db and files from the VCF
    l = GeminiLoader(args)
    l.populate_from_vcf()
    if not args.no_genotypes and not args.no_load_genotypes:
        l.store_sample_gt_counts()
    return l
Exemplo n.º 2
0
def load_singlecore(args):
    # create a new gemini loader and populate
    # the gemini db and files from the VCF
    l = GeminiLoader(args)
    l.populate_from_vcf()
    if not args.no_genotypes and not args.no_load_genotypes:
        l.store_sample_gt_counts()
    return l
Exemplo n.º 3
0
def finish(args, loader=None):
    """
    all things that are performed by single core, multi, ipython
    should be done here
    """
    if loader is None:
        loader = GeminiLoader(args, prepare_db=False)

    print("storing version, header, etc.")
    loader.store_resources()
    loader.store_version()
    loader.store_vcf_header()

    if not args.skip_gene_tables:
        print("storing gene-detailed")
        loader._get_gene_detailed()
        print("storing gene-summary")
        loader._get_gene_summary()
        if not args.test_mode:
            print("updating gene-table")
            loader.update_gene_table()
    if not args.test_mode:
        print("building indices")
        loader.build_indices_and_disconnect()
    else:
        from gemini import database
        database.close_and_commit(loader.c)
Exemplo n.º 4
0
def finish(args, loader=None):
    """
    all things that are performed by single core, multi, ipython
    should be done here
    """
    if loader is None:
        loader = GeminiLoader(args, prepare_db=False)

    print("storing version, header, etc.")
    loader.store_resources()
    loader.store_version()
    loader.store_vcf_header()

    if not args.skip_gene_tables:
        print("storing gene-detailed")
        loader._get_gene_detailed()
        print("storing gene-summary")
        loader._get_gene_summary()
        if not args.test_mode:
            print("updating gene-table")
            loader.update_gene_table()
    if not args.test_mode:
        print("building indices")
        loader.build_indices_and_disconnect()
    else:
        from gemini import database
        database.close_and_commit(loader.c)