def run_file_list_integration_test(self):
test_directory = os.path.dirname(os.path.abspath(__file__))
self.test_data_dir = os.path.join(test_directory, 'test_data', 'lsort')
# glob vcfs
vcfs = list()
for sample in ('NA12878', 'NA12891', 'NA12892'):
vcfs.append(os.path.join(self.test_data_dir, '{0}.sv.vcf.gz'.format(sample)))
expected_result = os.path.join(self.test_data_dir, 'lsort_expected')
temp_descriptor, temp_output_path = tempfile.mkstemp(suffix='.vcf')
with os.fdopen(temp_descriptor, 'w') as output_handle:
sorter = lsort.Lsort(vcfs, tempdir=None, batchsize=2, include_ref=False, output_handle=output_handle)
sorter.execute()
output_handle.flush()
expected_lines = open(expected_result).readlines()
produced_lines = open(temp_output_path).readlines()
diff = difflib.unified_diff(produced_lines, expected_lines, fromfile=temp_output_path, tofile=expected_result)
result = ''.join(diff)
if result != '':
for line in result:
sys.stdout.write(line)
self.assertFalse(result)
os.remove(temp_output_path)
def test_lsort_init_full(self):
file_list = ['file1', 'file2']
lsort_class = lsort.Lsort(file_list, tempdir='tempydir', batchsize=5)
self.assertEqual(lsort_class.vcf_file_names, file_list)
self.assertEqual(lsort_class.batchsize, 5)
self.assertEqual(lsort_class.tempdir, 'tempydir')
def test_lsort_init_defaults(self):
file_list = ['file1', 'file2']
lsort_class = lsort.Lsort(file_list)
self.assertEqual(lsort_class.vcf_file_names, file_list)
self.assertEqual(lsort_class.batchsize, 200)
self.assertEqual(lsort_class.tempdir, gettempdir())