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')
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,
)
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)
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,
)
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)
