def reader(self):
reader = infer_type.MSFileLoader(self.path)
assert len(reader.index) == 3
assert reader.index.from_index(0) == scan_ids[0]
assert list(reader.index.index_sequence) == sorted(
reader.index.index_sequence, key=lambda x: x[1])
return reader
def test_compat(self):
raw_reader = self.reader
mzml_reader = infer_type.MSFileLoader(self.reference_mzml)
mgf_reader = infer_type.MSFileLoader(self.reference_mgf)
mgf_scan = next(mgf_reader)
mzml_scan = mzml_reader[2]
raw_scan = raw_reader[2]
self.assertEqual(mzml_scan, raw_scan)
mgf_scan.pick_peaks()
raw_scan.pick_peaks()
self.assertEqual(raw_scan.peak_set, mgf_scan.peak_set)
self.assertEqual(raw_scan.precursor_information.precursor,
mzml_scan.precursor_information.precursor)
def reader(self):
reader = infer_type.MSFileLoader(self.path)
assert len(reader.index) == 3
assert reader.index.from_index(0) == scan_ids[0]
assert list(reader.index.index_sequence) == sorted(
reader.index.index_sequence, key=lambda x: x[1])
assert reader.source_file_name.endswith("three_test_scans.mzML")
return reader
def test_source_file_parsing(self):
reader = self.reader
finfo = reader.file_description()
sf = finfo.source_files[0]
assert sf.name == 'three_test_scans.mzML'
assert isinstance(sf.path, str)
reader = infer_type.MSFileLoader(self.only_ms2_path)
finfo = reader.file_description()
sf = finfo.source_files[0]
assert sf.name == 'analysis.baf'
assert isinstance(sf.path, str)
def test_infer_loader(self):
reader = infer_type.MSFileLoader(self.mzml_path)
self.assertIsNotNone(next(reader))
def reader(self):
return infer_type.MSFileLoader(self.path)
def test_software_list(self):
reader = infer_type.MSFileLoader(self.path)
assert len(reader.software_list()) == 2
def test_data_processing_parsing(self):
reader = infer_type.MSFileLoader(self.only_ms2_path)
assert len(reader.data_processing()[0]) == 3
def test_iteration_mode_detection(self):
reader = infer_type.MSFileLoader(self.only_ms2_path)
assert reader.iteration_mode == 'single'
def test_infer_loader_compressed(self):
reader = infer_type.MSFileLoader(self.mzmlgz_path)
assert reader.source_file_name is not None
self.assertIsNotNone(next(reader))
def test_infer(self):
reader = infer_type.MSFileLoader(self.path)
assert isinstance(reader, MzMLbLoader)
def setUpClass(cls):
cls.reader = MzMLbLoader(cls.path)
cls.reference_reader = infer_type.MSFileLoader(cls.ref_path)
super(TestMzMLbLoaderScanBehavior, cls).setUpClass()
