示例#1
0
def export_xls_pos(
    chrom,
    begin_pos,
    end_pos,
    sa_tab_csv_file,
    vcf_tabix_file,
    family_file,
    output_dir,
    report_code=None,
):
    if not os.path.exists(output_dir):
        os.makedirs(output_dir)
    if report_code is None:
        report_code = 'chr' + str(chrom)
    ma = MutationAnnotator(report_code)
    db_man = DBManager()
    db_man.connect_summarize_annovar_db(sa_tab_csv_file)
    db_man.connect_vcf_db(vcf_tabix_file, chrom, begin_pos, end_pos)
    db_man.connect_family_db(family_file)
    ma.db_manager = db_man
    ma.export_xls(output_dir)