Exemple #1
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:
        import database
        database.close_and_commit(loader.c)
Exemple #2
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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:
        import database
        database.close_and_commit(loader.c)
Exemple #3
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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.populate_from_vcf()
    gemini_loader.build_indices_and_disconnect()

    if not args.no_genotypes and not args.no_load_genotypes:
        gemini_loader.store_sample_gt_counts()
Exemple #4
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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.populate_from_vcf()
    gemini_loader.build_indices_and_disconnect()

    if not args.no_genotypes and not args.no_load_genotypes:
        gemini_loader.store_sample_gt_counts()
Exemple #5
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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.populate_from_vcf()

    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()
    gemini_annotate.add_extras(args.db, [args.db])
Exemple #6
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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.populate_from_vcf()

    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()
    gemini_annotate.add_extras(args.db, [args.db])