def test_decoding(self):
with MzML(self.path, decode_binary=True) as reader:
spectrum = next(reader)
self.assertIsNotNone(spectrum['m/z array'])
validation = spectrum['m/z array']
with MzML(self.path) as reader:
spectrum = next(reader)
self.assertIsNotNone(spectrum['m/z array'])
self.assertTrue(np.allclose(spectrum['m/z array'], validation))
with MzML(self.path, decode_binary=False) as reader:
spectrum = next(reader)
record = spectrum['m/z array']
self.assertEqual(record.compression, "no compression")
self.assertEqual(record.dtype, np.float64)
array = record.decode()
self.assertTrue(np.allclose(validation, array))
record = spectrum['intensity array']
self.assertEqual(record.dtype, np.float32)
self.assertEqual(record.compression, "no compression")
spectrum = next(reader)
record = spectrum['intensity array']
self.assertEqual(record.compression, "zlib compression")
self.assertEqual(mzml_spectra[1]['intensity array'],
record.decode())
def test_in_memory_buffer(self):
with open(self.path, 'rb') as fh:
data_buffer = BytesIO(fh.read())
with MzML(data_buffer) as reader:
spectrum = next(reader)
self.assertEqual(spectrum['id'], 'controllerType=0 controllerNumber=1 scan=1')
data_buffer.seek(0)
with MzML(data_buffer, use_index=True) as reader:
spectrum = next(reader)
self.assertEqual(spectrum['id'], 'controllerType=0 controllerNumber=1 scan=1')
def test_retrieve_refs(self):
with MzML(self.path) as reader:
derefed = list(reader.iterfind("instrumentConfiguration", retrieve_refs=True))
reader.reset()
raw = list(reader.iterfind("instrumentConfiguration", retrieve_refs=False))
self.assertEqual(raw[0].get("ref"), 'CommonInstrumentParams')
self.assertNotIn("ref", derefed[0])
self.assertEqual(derefed[0].get('instrument serial number'), 'SN06061F')
def test_unit_extract(self):
with MzML(self.path) as handle:
for scan in handle:
scan_inst = scan['scanList']['scan'][0]
scan_time = scan_inst['scan start time']
scan_window_lower_limit = scan_inst['scanWindowList']['scanWindow'][0]['scan window lower limit']
self.assertEqual(scan_time.unit_info, 'minute')
self.assertEqual(scan_window_lower_limit.unit_info, 'm/z')
def test_cv_query(self):
with MzML(self.path) as handle:
scan = next(handle)
index = aux.cvquery(scan)
self.assertEqual(index['MS:1000511'], 1)
self.assertEqual(aux.cvquery(scan, "MS:1000511"), 1)
# test deep traversal
self.assertEqual(index['MS:1000016'], 0.004935)
self.assertEqual(aux.cvquery(scan, 'MS:1000016'), 0.004935)
def test_prebuild_index(self):
test_dir = tempfile.mkdtemp()
work_path = os.path.join(test_dir, self.path)
with open(work_path, 'w') as dest, open(self.path) as source:
dest.write(source.read())
assert dest.closed
with MzML(work_path, use_index=False) as inst:
self.assertRaises(IOError, inst._read_byte_offsets)
with open(inst._byte_offset_filename, 'wt') as fh:
fh.write("{}")
self.assertRaises(TypeError, inst._read_byte_offsets)
os.remove(inst._byte_offset_filename)
with MzML(work_path, use_index=True) as inst:
offsets_exist = os.path.exists(inst._byte_offset_filename)
self.assertEqual(offsets_exist, inst._check_has_byte_offset_file())
self.assertTrue(isinstance(inst._offset_index, xml.HierarchicalOffsetIndex))
self.assertTrue(inst._source.closed)
MzML.prebuild_byte_offset_file(work_path)
with open(inst._byte_offset_filename, 'rt') as fh:
index = MzML._index_class.load(fh)
assert inst._offset_index['spectrum'] == index['spectrum']
with MzML(work_path, use_index=True) as inst:
offsets_exist = os.path.exists(inst._byte_offset_filename)
self.assertTrue(offsets_exist)
self.assertEqual(offsets_exist, inst._check_has_byte_offset_file())
self.assertTrue(isinstance(inst._offset_index, xml.HierarchicalOffsetIndex))
self.assertTrue(inst._source.closed)
os.remove(inst._byte_offset_filename)
with MzML(work_path, use_index=True) as inst:
offsets_exist = os.path.exists(inst._byte_offset_filename)
self.assertEqual(offsets_exist, inst._check_has_byte_offset_file())
self.assertTrue(isinstance(inst._offset_index, xml.HierarchicalOffsetIndex))
self.assertTrue(inst._source.closed)
shutil.rmtree(test_dir, True)
def test_indexing(self):
with MzML(self.path) as reader:
self.assertEqual(mzml_spectra[0], reader[0])
self.assertEqual(mzml_spectra[0], reader['controllerType=0 controllerNumber=1 scan=1'])
self.assertEqual(mzml_spectra, reader[0:2])
self.assertEqual(mzml_spectra,
[reader['controllerType=0 controllerNumber=1 scan=1'],
reader['controllerType=0 controllerNumber=1 scan=2']])
self.assertEqual(mzml_spectra, reader[[0, 1]])
self.assertEqual(mzml_spectra, reader[
['controllerType=0 controllerNumber=1 scan=1', 'controllerType=0 controllerNumber=1 scan=2']])
self.assertEqual(mzml_spectra, reader[
'controllerType=0 controllerNumber=1 scan=2':'controllerType=0 controllerNumber=1 scan=1'])
def open(self):
"""Open the mzML file for reading"""
return MzML(str(self.path))
def test_map_qsize(self):
key = op.itemgetter('index')
with MzML(self.path, queue_size=1000) as f:
self.assertEqual(f._queue_size, 1000)
self.assertEqual(sorted(mzml_spectra, key=key), sorted(list(f.map()), key=key))
def test_mp_requires_index(self):
with MzML(self.path, use_index=False) as r:
self.assertRaises(aux.PyteomicsError, r.map)
def test_mp_read(self):
key = op.itemgetter('index')
with MzML(self.path) as f:
self.assertEqual(sorted(mzml_spectra, key=key), sorted(list(f.map()), key=key))
def test_time_locator(self):
with MzML(self.path) as reader:
self.assertEqual(mzml_spectra[0], reader.time[0])
self.assertEqual(mzml_spectra[1], reader.time[0.1])
self.assertEqual(mzml_spectra, reader.time[0:0.1])
def test_picklable(self):
with MzML(self.path) as reader:
expected_data = next(reader)
spec = pickle.dumps(reader)
with pickle.loads(spec) as reader:
self.assertEqual(next(reader)['id'], expected_data['id'])