def test_compress_in_place(self, mock_pbar):
for input_file in os.listdir(os.path.join(test_data, 'single_reads')):
# We copy file by file as copytree won't work to an existing directory
shutil.copy(os.path.join(test_data, 'single_reads', input_file),
self.save_path)
self.assertCompressed(self.save_path, GZIP, read_count=4, file_count=4)
in_files = set(os.listdir(self.save_path))
compress_batch(self.save_path,
output_folder=None,
target_compression=VBZ,
in_place=True)
self.assertCompressed(self.save_path, VBZ, read_count=4, file_count=4)
self.assertEqual(in_files, set(os.listdir(self.save_path)))
def test_conversion_script_multi(self, mock_pbar):
input_folder = os.path.join(test_data, 'multi_read')
compress_batch(input_folder=input_folder,
output_folder=self.save_path,
target_compression=VBZ)
count_files = 0
count_reads = 0
for out_file in get_fast5_file_list(self.save_path,
recursive=True,
follow_symlinks=True):
count_files += 1
with get_fast5_file(out_file) as f5:
self.assertTrue(isinstance(f5, MultiFast5File))
for read in f5.get_reads():
self.assertCompressed(read)
count_reads += 1
self.assertEqual(1, count_files)
self.assertEqual(4, count_reads)
def test_conversion_script_single(self, mock_pbar):
input_folder = os.path.join(test_data, 'single_reads')
compress_batch(input_folder=input_folder,
output_folder=self.save_path,
target_compression=VBZ)
self.assertCompressed(self.save_path, VBZ, read_count=4, file_count=4)