def test_error_new_field_no_description(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'input.vcf'),
os.path.join(self.test_data_dir, 'info.tsv'),
'TEST',
'-o', 'ztest.vcf'
]
vcf_info_annotator.main(command)
self.assertTrue("the --description and --value_format arguments are required unless updating/overwriting an existing field (with flag --overwrite)" in str(context.exception))
def test_overwrite_when_field_doesnt_exist(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'input.vcf'),
os.path.join(self.test_data_dir, 'info.tsv'),
'TEST',
'-o', 'ztest.vcf',
'-w'
]
vcf_info_annotator.main(command)
self.assertTrue("INFO field TEST does not exist and thus cannot be overwritten!" in str(context.exception))
def test_error_already_INFO_annotated(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'input.vcf'),
os.path.join(self.test_data_dir, 'info.tsv'),
'CSQ',
'-d', "test",
'-f', 'Integer',
'-o', 'ztest.vcf'
]
vcf_info_annotator.main(command)
self.assertTrue('INFO already contains a CSQ field. Choose a different label, or use the --overwrite flag to retain this field and overwrite values' in str(context.exception))
def test_addwhile_overwriteset(self):
temp_path = tempfile.TemporaryDirectory()
print(temp_path)
command = [
os.path.join(self.test_data_dir, 'info2_input.vcf'),
os.path.join(self.test_data_dir, 'info2.tsv'),
'MQ0',
'-w',
'-o', os.path.join(temp_path.name, 'info2_output.vcf')
]
vcf_info_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'info2_output.vcf'), os.path.join(temp_path.name, 'info2_output.vcf')))
temp_path.cleanup()
def test_simple_string(self):
temp_path = tempfile.TemporaryDirectory()
print(temp_path)
command = [
os.path.join(self.test_data_dir, 'input.vcf'),
os.path.join(self.test_data_dir, 'info3.tsv'),
'TEST',
'-d', "test",
'-f', 'String',
'-o', os.path.join(temp_path.name, 'info3_output.vcf')
]
vcf_info_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'info3_output.vcf'), os.path.join(temp_path.name, 'info3_output.vcf')))
temp_path.cleanup()
def test_overwrite_existing_field(self):
temp_path = tempfile.TemporaryDirectory()
print(temp_path)
command = [
os.path.join(self.test_data_dir, 'input.vcf'),
os.path.join(self.test_data_dir, 'info.tsv'),
'CSQ',
'-d', "test",
'-f', 'Integer',
'-w',
'-o', os.path.join(temp_path.name, 'info_annotation.vcf')
]
vcf_info_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'info_overwrite.vcf'), os.path.join(temp_path.name, 'info_annotation.vcf')))
temp_path.cleanup()