def test_compress_read_from_single(self):
with get_fast5_file(os.path.join(test_data, "single_reads", "read0.fast5"), "r") as input_f5, \
EmptyFast5(self.generate_temp_filename(), 'w') as output_f5:
read_id = input_f5.get_read_ids()[0]
input_read = input_f5.get_read(read_id)
# Input read should be uncompressed on the way in:
self.assertEqual(check_read_compression(input_read), GZIP)
compress_single_read(output_f5, input_read, target_compression=VBZ)
output_read = output_f5.get_read(read_id)
self.assertEqual(check_read_compression(output_read), VBZ)
def test_add_read_from_multi(self):
target_compression = VBZ
with get_fast5_file(os.path.join(test_data, "multi_read", "batch_0.fast5"), "r") as input_f5, \
MultiFast5File(self.generate_temp_filename(), 'w') as output_f5:
read_id = input_f5.get_read_ids()[0]
input_read = input_f5.get_read(read_id)
# Input read should be uncompressed on the way in:
self.assertEqual(check_read_compression(input_read), GZIP)
output_f5.add_existing_read(input_read, target_compression)
output_read = output_f5.get_read(read_id)
self.assertEqual(check_read_compression(output_read), VBZ)
def test_check_read_compression_vbz(self):
with get_fast5_file(os.path.join(test_data, 'vbz_reads', 'vbz_reads.fast5'), 'r') as f5:
for read in f5.get_reads():
compression = check_read_compression(read)
self.assertEqual(compression, VBZ)
def test_check_read_compression_multi_read(self):
with get_fast5_file(os.path.join(test_data, 'multi_read', 'batch_0.fast5'), 'r') as f5:
for read in f5.get_reads():
compression = check_read_compression(read)
self.assertEqual(compression, GZIP)