def test_summarize_annovar3(self):
self.individual_debug = True
""" to test if summarize can run for one whole vcf file """
self.init_test(self.current_func_name)
test_tabix_file = os.path.join(self.data_dir,
self.current_func_name + '.vcf.gz')
test_working_dir = self.working_dir
test_out_prefix = 'test_summarize_annovar3_out'
summarize_annovar(test_tabix_file,
test_working_dir,
test_out_prefix,
)
expected_tmp_avdb_file = os.path.join(self.data_dir,
'expected_tmp_avdb3')
tmp_avdb_file = os.path.join(test_working_dir,
test_out_prefix + '_tmp_avdb')
self.assertTrue(filecmp.cmp(tmp_avdb_file,
expected_tmp_avdb_file),
"avdb file is incorrectly prepared")
expected_avdb_file = os.path.join(self.data_dir,
'expected_avdb3')
avdb_file = os.path.join(test_working_dir,
test_out_prefix + '.avdb')
self.assertTrue(filecmp.cmp(avdb_file,
expected_avdb_file),
"avdb file is incorrectly produced")
expected_tab_csv_file = os.path.join(self.data_dir,
'expected_tab_csv3')
tab_csv_file = os.path.join(test_working_dir,
test_out_prefix + '.tab.csv')
self.assertTrue(filecmp.cmp(tab_csv_file,
expected_tab_csv_file),
"incorrect csv output file")
def generate_summarize_annovar_db_chr9_axeq():
summarize_annovar(
'9',
'1',
'106000000',
AXEQ_VCF_TABIX_FILE,
GLOBAL_WORKING_DIR,
'chr9_axeq',
)
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 test_summarize_annovar2(self):
# self.individual_debug = True
self.init_test(self.current_func_name)
test_chrom = '18'
test_begin_pos = '12512250'
test_end_pos = '14513600'
test_tabix_file = os.path.join(self.data_dir,
self.current_func_name + '.vcf.gz')
test_working_dir = self.working_dir
test_out_prefix = 'test_summarize_annovar2_out'
summarize_annovar(test_tabix_file,
test_working_dir,
test_out_prefix,
test_chrom,
test_begin_pos,
test_end_pos,
)
expected_tmp_avdb_file = os.path.join(self.data_dir,
'expected_tmp_avdb2')
tmp_avdb_file = os.path.join(test_working_dir,
test_out_prefix + '_tmp_avdb')
self.assertTrue(filecmp.cmp(tmp_avdb_file,
expected_tmp_avdb_file),
"avdb file is incorrectly prepared")
expected_avdb_file = os.path.join(self.data_dir,
'expected_avdb2')
avdb_file = os.path.join(test_working_dir,
test_out_prefix + '.avdb')
self.assertTrue(filecmp.cmp(avdb_file,
expected_avdb_file),
"avdb file is incorrectly produced")
expected_tab_csv_file = os.path.join(self.data_dir,
'expected_tab_csv2')
tab_csv_file = os.path.join(test_working_dir,
test_out_prefix + '.tab.csv')
self.assertTrue(filecmp.cmp(tab_csv_file,
expected_tab_csv_file),
"incorrect csv output file")
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)
def generate_summarize_annovar_db_scilife():
summarize_annovar(SCILIFE_VCF_TABIX_FILE, GLOBAL_WORKING_DIR, "scilife")
def generate_summarize_annovar_db_chr9_axeq():
summarize_annovar(AXEQ_VCF_TABIX_FILE, GLOBAL_WORKING_DIR, "chr9_axeq", "9", "1", "106000000")