def test_error_missing_column_in_tsv(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'input.vcf.gz'),
'Consequence',
'-t', os.path.join(self.test_data_dir, 'variants.no_ALT.tsv'),
]
vep_annotation_reporter.main(command)
self.assertTrue("doesn't contain required column 'ALT'." in str(context.exception))
def test_error_no_vep_annotation(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, '..', 'no_csq.vcf'),
'Consequence',
'-t', os.path.join(self.test_data_dir, 'variants.tsv'),
]
vep_annotation_reporter.main(command)
self.assertTrue('is not VEP-annotated. Please annotate the VCF with VEP before running this tool.' in str(context.exception))
def test_no_input_tsv(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.vcf.gz'), os.path.join(temp_path.name, 'input.vcf.gz'))
command = [
os.path.join(temp_path.name, 'input.vcf.gz'),
'Consequence',
]
vep_annotation_reporter.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.no_input_tsv.tsv'), os.path.join(temp_path.name, 'input.tsv')))
temp_path.cleanup()
def test_vcf_with_multiple_transcripts_and_no_pick(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.merge_multiple_transcripts.vcf.gz'), os.path.join(temp_path.name, 'input.vcf.gz'))
command = [
os.path.join(temp_path.name, 'input.vcf.gz'),
'SYMBOL',
]
vep_annotation_reporter.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.merge_multiple_transcripts.tsv'), os.path.join(temp_path.name, 'input.tsv')))
temp_path.cleanup()
def test_vcf_entries_with_no_csq_runs_successfully(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.variants_without_csq.vcf.gz'), os.path.join(temp_path.name, 'input.vcf.gz'))
command = [
os.path.join(temp_path.name, 'input.vcf.gz'),
'Consequence',
]
vep_annotation_reporter.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.variants_without_csq.tsv'), os.path.join(temp_path.name, 'input.tsv')))
temp_path.cleanup()
def test_multiple_multiallelic_site(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, '..', 'input.multiallelic.vcf.gz'), os.path.join(temp_path.name, 'input.vcf.gz'))
command = [
os.path.join(temp_path.name, 'input.vcf.gz'),
'Consequence',
'-t', os.path.join(self.test_data_dir, 'variants.multiallelic.tsv'),
]
vep_annotation_reporter.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.multiallelic.tsv'), os.path.join(temp_path.name, 'input.tsv')))
temp_path.cleanup()
def test_nonexistent_vep_field(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.vcf.gz'), os.path.join(temp_path.name, 'input.vcf.gz'))
command = [
os.path.join(temp_path.name, 'input.vcf.gz'),
'Nonexistent_Field',
'-t', os.path.join(self.test_data_dir, 'variants.tsv'),
]
vep_annotation_reporter.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.nonexistent_field.tsv'), os.path.join(temp_path.name, 'input.tsv')))
temp_path.cleanup()