def test_get_region_chrom(self):
        """

        to see if get_region_chrom can manage to find the correct reference file
        and it can correct read begin position and end position for
        the given biomarkers

        """

        self.init_test(self.current_func_name)
        test_ref_db_prefix = os.path.join(self.data_dir,
                                          self.current_func_name)
        test_chrom = '18'
        test_begin_marker = 'rs146647843'
        test_end_marker = 'rs117978838'
        (begin_pos, end_pos) = get_region_chrom(test_chrom,
                                                test_begin_marker,
                                                test_end_marker,
                                                test_ref_db_prefix,
                                                )
        self.assertEqual(begin_pos,
                         '12697297',
                         'Incorrect begin position')
        self.assertEqual(end_pos,
                         '12951877',
                         'Incorrect end position')
예제 #2
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def export_xls(
    chrom,
    begin_marker,
    end_marker,
    sa_tab_csv_file,
    vcf_tabix_file,
    family_file,
    output_dir,
    report_code=None,
):
    (begin_pos, end_pos) = get_region_chrom(
        chrom,
        begin_marker,
        end_marker,
        REF_DB_FILE_PREFIX,
    )
    export_xls_pos(
        chrom,
        begin_pos,
        end_pos,
        sa_tab_csv_file,
        vcf_tabix_file,
        family_file,
        output_dir,
        report_code=None,
    )
예제 #3
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def generate_summarize_annovar_db(chrom, begin_marker, end_marker,
                                  tabix_vcf_file, working_dir, out_prefix):
    (begin_pos, end_pos) = get_region_chrom(
        chrom,
        begin_marker,
        end_marker,
        REF_DB_FILE_PREFIX,
    )
    summarize_annovar(chrom, begin_pos, end_pos, tabix_vcf_file, working_dir,
                      out_prefix)
예제 #4
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def export_xls(
    sa_tab_csv_file, vcf_tabix_file, family_file, output_dir, report_code=None, chrom="", begin_marker="", end_marker=""
):
    (begin_pos, end_pos) = get_region_chrom(chrom, begin_marker, end_marker, REF_DB_FILE_PREFIX)
    export_xls_pos(
        sa_tab_csv_file,
        vcf_tabix_file,
        family_file,
        output_dir,
        report_code=None,
        chrom=chrom,
        begin_pos=begin_pos,
        end_pos=end_pos,
    )
예제 #5
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def generate_summarize_annovar_db(tabix_vcf_file, out_prefix, chrom, begin_marker, end_marker):
    if chrom != "":
        (begin_pos, end_pos) = get_region_chrom(chrom, begin_marker, end_marker, REF_DB_FILE_PREFIX)
    summarize_annovar(tabix_vcf_file, GLOBAL_WORKING_DIR, out_prefix, chrom, begin_pos, end_pos)