def test_error_more_than_one_sample_without_sample_name(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'multiple_samples.vcf'),
os.path.join(self.test_data_dir, 'snvs.bam_readcount'),
'DNA',
]
vcf_readcount_annotator.main(command)
self.assertTrue('contains more than one sample. Please use the -s option to specify which sample to annotate.' in str(context.exception))
def test_error_more_than_one_sample_with_wrong_sample_name(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'multiple_samples.vcf'),
os.path.join(self.test_data_dir, 'snvs.bam_readcount'),
'DNA',
'-s', 'nonexistent_sample',
]
vcf_readcount_annotator.main(command)
self.assertTrue('does not contain a sample column for sample nonexistent_sample.' in str(context.exception))
def test_input_AF_is_of_number_1(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'af_number_1.vcf'),
os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'af_number_1.bam-readcount.tsv'),
'DNA', '-s', 'TUMOR'
]
vcf_readcount_annotator.main(command)
def test_mutation_without_matching_readcount_value(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'no_matching_readcount.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'snvs.bam_readcount'),
'DNA',
]
vcf_readcount_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'no_matching_readcount.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
temp_path.cleanup()
def test_single_sample_vcf_with_existing_readcount_annotations(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.readcount.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'snvs.bam_readcount'),
'DNA',
]
vcf_readcount_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'single_sample_with_existing_readcount_annotations.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
temp_path.cleanup()
def test_error_duplicate_bam_readcount_entries(self):
with self.assertRaises(Exception) as context:
command = [
os.path.join(self.test_data_dir, 'multiple_samples.vcf'),
os.path.join(self.test_data_dir, 'duplicate.bam_readcount'),
'DNA',
]
vcf_readcount_annotator.main(command)
self.assertTrue(
"Duplicate bam-readcount entry for chr 22 pos 16202096 ref C:" in
str(context.exception))
def test_multi_sample_vcf(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'multiple_samples.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'snvs.bam_readcount'),
'DNA',
'-s', 'H_NJ-HCC1395-HCC1395',
]
vcf_readcount_annotator.main(command)
self.assertTrue(cmp(os.path.join(self.test_data_dir, 'multiple_samples.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
temp_path.cleanup()
def test_hom_ref_genotype(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'hom_ref.vcf'),
os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'hom_ref.bam_readcount'), 'DNA',
'-s', 'NORMAL'
]
vcf_readcount_annotator.main(command)
self.assertTrue(
cmp(os.path.join(self.test_data_dir, 'hom_ref.readcount.vcf'),
os.path.join(temp_path.name, 'input.readcount.vcf')))
temp_path.cleanup()
def test_multiple_bam_readcount_files(self):
temp_path = tempfile.TemporaryDirectory()
os.symlink(
os.path.join(self.test_data_dir, 'input.snvs_and_indels.vcf'),
os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'snvs.bam_readcount'),
os.path.join(self.test_data_dir, 'indels.bam_readcount'),
'DNA',
]
vcf_readcount_annotator.main(command)
self.assertTrue(
cmp(
os.path.join(
self.test_data_dir,
'multiple_bam_readcount_files.zero.readcount.vcf'),
os.path.join(temp_path.name, 'input.readcount.vcf')))
temp_path.cleanup()