def test_cleaning_up_temporary_files(batch_size):
input_paths, _, temp_dir = setup_func()
with NamedTemporaryFile('w+') as outfile:
ivcfmerge_batch(input_paths, outfile.name, batch_size, temp_dir)
# Will throw exception if not empty
Path(temp_dir).rmdir()
def test_custom_temporary_directory(batch_size):
input_paths, ref_merged_path, temp_dir = setup_func()
with NamedTemporaryFile('w+') as outfile, open(ref_merged_path, 'r') as ref_merged:
ivcfmerge_batch(input_paths, outfile.name, batch_size, temp_dir)
output = outfile.read()
assert output == ref_merged.read()
def test_merging_example_input(batch_size):
input_paths, ref_merged_path, _ = setup_func()
with NamedTemporaryFile('w+') as outfile, open(ref_merged_path, 'r') as ref_merged:
ivcfmerge_batch(input_paths, outfile.name, batch_size)
output = outfile.read()
assert output == ref_merged.read()
def test_not_cleaning_up_other_files(batch_size):
input_paths, _, temp_dir = setup_func()
(Path(temp_dir) / 'other').touch()
with NamedTemporaryFile('w+') as outfile:
ivcfmerge_batch(input_paths, outfile.name, batch_size, temp_dir)
with pytest.raises(OSError):
Path(temp_dir).rmdir()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--batch-size', type=int)
parser.add_argument('--temp-dir', type=str)
parser.add_argument('input_paths_file', type=str)
parser.add_argument('output_path', type=str)
args = parser.parse_args()
with open(args.input_paths_file, 'r') as input_paths_file:
input_paths = input_paths_file.read().splitlines()
ivcfmerge_batch(input_paths, args.output_path, args.batch_size,
args.temp_dir)
def test_not_cleaning_up_temporary_directory_in_failures(batch_size):
input_paths, _, temp_dir = setup_func()
expected_error = Exception
def write_file(temp_dir):
open(Path(temp_dir) / 'random', 'w')
with mock.patch('ivcfmerge.batch._ivcfmerge', side_effect=[write_file(temp_dir), expected_error]),\
NamedTemporaryFile('w+') as outfile, pytest.raises(expected_error):
ivcfmerge_batch(input_paths, outfile.name, batch_size, temp_dir)
with pytest.raises(OSError):
Path(temp_dir).rmdir()
def test_single_input_yields_the_same_output_as_normal_ivcfmerge(batch_size):
input_paths = ['tests/data/input/1.vcf']
with ExitStack() as stack:
files = map(lambda fn: stack.enter_context(open(fn)), input_paths)
with TemporaryFile('w+') as outfile:
ivcfmerge(files, outfile)
outfile.seek(0)
expected = outfile.read()
with NamedTemporaryFile('w+') as outfile:
ivcfmerge_batch(input_paths, outfile.name, batch_size)
output = outfile.read()
assert output == expected
def test_out_of_bound_batch_sizes_yield_the_same_output_as_normal_ivcfmerge(batch_size):
input_paths, _, _ = setup_func()
with ExitStack() as stack:
files = map(lambda fn: stack.enter_context(open(fn)), input_paths)
with TemporaryFile('w+') as outfile:
ivcfmerge(files, outfile)
outfile.seek(0)
expected = outfile.read()
with NamedTemporaryFile('w+') as outfile:
ivcfmerge_batch(input_paths, outfile.name, batch_size)
output = outfile.read()
assert output == expected