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()