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import h5py
import numpy
import os
import unittest
TEST_DATA = os.path.join(os.path.dirname(__file__), "..", "..", "test_data")
class TestVbzFilter(unittest.TestCase):
VBZ_VERISON = 0
def test_simple_range(self):
original_data = numpy.arange(1, 100, dtype="i2")
with h5py.File("test_file.h5", "w") as f:
f.create_dataset("bar", compression=32020, compression_opts=(self.VBZ_VERISON, 2, 1, 1), data=original_data)
with h5py.File("test_file.h5", "r") as f:
numpy.testing.assert_array_equal(f["bar"][:], original_data)
def test_compressing_real_data(self):
zip_file = h5py.File(os.path.join(TEST_DATA, "multi_fast5_zip.fast5"))
for zip_key in zip_file.keys():
original_data = zip_file[zip_key]["Raw/Signal"][:]
if (zip_key == "read_008468c3-e477-46c4-a6e2-7d021a4ebf0b"):
continue
with h5py.File("test_file.h5", "w") as f:
f.create_dataset("bar", compression=32020, compression_opts=(self.VBZ_VERISON, 2, 1, 1), data=original_data, chunks=(len(original_data),))
with h5py.File("test_file.h5", "r") as f:
numpy.testing.assert_array_equal(f["bar"][:], original_data)
class TestVbzFilterV0(TestVbzFilter):
VBZ_VERISON = 0
class TestVbzFilterV1(TestVbzFilter):
VBZ_VERISON = 1
class TestVbzStoredFiles(unittest.TestCase):
def test_stored_files(self):
files = [
h5py.File(os.path.join(TEST_DATA, "multi_fast5_zip.fast5")),
h5py.File(os.path.join(TEST_DATA, "multi_fast5_vbz.fast5")),
h5py.File(os.path.join(TEST_DATA, "multi_fast5_vbz_v1.fast5")),
]
for sorted_keys in zip(*[sorted(file.keys()) for file in files ]):
for e in sorted_keys[1:]:
self.assertEqual(sorted_keys[0], e)
key = sorted_keys[0]
first_data = files[0][key]["Raw/Signal"][:]
for file in files[1:]:
data = file[key]["Raw/Signal"][:]
numpy.testing.assert_array_equal(first_data, data)
if __name__ == '__main__':
unittest.main()
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