From 0ed85b864c69975cc1852ce07df144cc7fb910ab Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 5 Oct 2023 12:51:19 +0200 Subject: [PATCH 1/9] fixed instrumentConfigurationRef missing --- spectrum_io/raw/msraw.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index 1b1826c..a800863 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -151,7 +151,7 @@ def read_mzml( for spec in data_iter: if spec["ms level"] != 1: # filter out ms1 spectra if there are any spec_id = spec["id"].split("scan=")[-1] - instrument_configuration_ref = spec["scanList"]["scan"][0]["instrumentConfigurationRef"] + instrument_configuration_ref = spec["scanList"]["scan"][0].get("instrumentConfigurationRef", "") fragmentation = spec["scanList"]["scan"][0]["filter string"].split("@")[1][:3].upper() mz_range = spec["scanList"]["scan"][0]["filter string"].split("[")[1][:-1] rt = spec["scanList"]["scan"][0]["scan start time"] @@ -163,7 +163,7 @@ def read_mzml( spec["m/z array"], mz_range, rt, - mass_analyzer[instrument_configuration_ref], + mass_analyzer.get(instrument_configuration_ref, "unknown"), fragmentation, ] data_iter.close() @@ -229,7 +229,7 @@ def _get_scans_pymzml( for spec in data_iter: if spec.ms_level != 1: # filter out ms1 spectra if there are any key = f"{file_name}_{spec.ID}" - instrument_configuration_ref = spec["scanList"]["scan"][0]["instrumentConfigurationRef"] + instrument_configuration_ref = spec["scanList"]["scan"][0].get("instrumentConfigurationRef", "") filter_string = str(spec.element.find(".//*[@accession='MS:1000512']").get("value")) fragmentation = filter_string.split("@")[1][:3].upper() mz_range = filter_string.split("[")[1][:-1] @@ -240,7 +240,7 @@ def _get_scans_pymzml( spec.mz, mz_range, spec.scan_time_in_minutes(), - mass_analyzer[instrument_configuration_ref], + mass_analyzer.get(instrument_configuration_ref, "unknown"), fragmentation, ] else: @@ -250,7 +250,7 @@ def _get_scans_pymzml( # https://github.com/pymzml/pymzML/blob/a883ff0e61fd97465b0a74667233ff594238e335/pymzml/file_classes # /standardMzml.py#L81-L84 key = f"{file_name}_{spec.ID}" - instrument_configuration_ref = spec["scanList"]["scan"][0]["instrumentConfigurationRef"] + instrument_configuration_ref = spec["scanList"]["scan"][0].get("instrumentConfigurationRef", "") filter_string = str(spec.element.find(".//*[@accession='MS:1000512']").get("value")) fragmentation = filter_string.split("@")[1][:3].upper() mz_range = filter_string.split("[")[1][:-1] @@ -261,7 +261,7 @@ def _get_scans_pymzml( spec.mz, mz_range, spec.scan_time_in_minutes(), - mass_analyzer[instrument_configuration_ref], + mass_analyzer.get(instrument_configuration_ref, "unknown"), fragmentation, ] data_iter.close() From d6994dc6ab4425e6a6333e89b80f7d571be85d51 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 24 Oct 2023 00:21:22 +0200 Subject: [PATCH 2/9] cleaned up and remove filter string --- spectrum_io/raw/msraw.py | 165 +++++++++++++++++++++++---------------- 1 file changed, 98 insertions(+), 67 deletions(-) diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index a800863..8dc7a46 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -135,38 +135,11 @@ def read_mzml( :return: pd.DataFrame with intensities and m/z values """ file_list = MSRaw.get_file_list(source, ext) - data = {} # type: Dict[str, Any] + if package == "pymzml": - with warnings.catch_warnings(): - warnings.filterwarnings("ignore", category=ImportWarning) - for file_path in file_list: - logger.info(f"Reading mzML file: {file_path}") - MSRaw._get_scans_pymzml(file_path, data, scanidx, *args, **kwargs) + data = MSRaw._read_mzml_pymzml(file_list, scanidx, *args, **kwargs) elif package == "pyteomics": - for file_path in file_list: - mass_analyzer = get_mass_analyzer(file_path) - logger.info(f"Reading mzML file: {file_path}") - data_iter = mzml.read(source=str(file_path), *args, **kwargs) - file_name = file_path.stem - for spec in data_iter: - if spec["ms level"] != 1: # filter out ms1 spectra if there are any - spec_id = spec["id"].split("scan=")[-1] - instrument_configuration_ref = spec["scanList"]["scan"][0].get("instrumentConfigurationRef", "") - fragmentation = spec["scanList"]["scan"][0]["filter string"].split("@")[1][:3].upper() - mz_range = spec["scanList"]["scan"][0]["filter string"].split("[")[1][:-1] - rt = spec["scanList"]["scan"][0]["scan start time"] - key = f"{file_name}_{spec_id}" - data[key] = [ - file_name, - spec_id, - spec["intensity array"], - spec["m/z array"], - mz_range, - rt, - mass_analyzer.get(instrument_configuration_ref, "unknown"), - fragmentation, - ] - data_iter.close() + data = MSRaw._read_mzml_pyteomics(file_list, *args, **kwargs) else: raise AssertionError("Choose either 'pymzml' or 'pyteomics'") @@ -174,6 +147,59 @@ def read_mzml( data["SCAN_NUMBER"] = pd.to_numeric(data["SCAN_NUMBER"]) return data + @staticmethod + def _read_mzml_pymzml(file_list: List[Path], scanidx: Optional[List] = None, *args, **kwargs) -> Dict[str, str]: + data = {} + with warnings.catch_warnings(): + warnings.filterwarnings("ignore", category=ImportWarning) + for file_path in file_list: + logger.info(f"Reading mzML file: {file_path}") + MSRaw._get_scans_pymzml(file_path, data, scanidx, *args, **kwargs) + + @staticmethod + def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> Dict[str, str]: + data = {} + for file_path in file_list: + mass_analyzer = get_mass_analyzer(file_path) + logger.info(f"Reading mzML file: {file_path}") + data_iter = mzml.read(source=str(file_path), *args, **kwargs) + file_name = file_path.stem + for spec in data_iter: + if spec["ms level"] != 2: + continue # filter out ms1 spectra if there are any + spec_id = spec["id"].split("scan=")[-1] + scan = spec["scanList"]["scan"][0] + instrument_configuration_ref = scan.get("instrumentConfigurationRef", "") + activation = spec["precursorList"]["precursor"][0]["activation"] + fragmentation = "unknown" + for key in activation.keys(): + if key == "collision energy": + pass + if "beam-type" in key: + fragmentation = "HCD" + break + if "collision-induced dissociation" in key: + fragmentation = "CID" + break + else: + fragmentation = key + scan_lower_limit = scan["scanWindowList"]["scanWindow"][0]["scan window lower limit"] + scan_upper_limit = scan["scanWindowList"]["scanWindow"][0]["scan window upper limit"] + mz_range = f"{scan_lower_limit}-{scan_upper_limit}" + rt = spec["scanList"]["scan"][0]["scan start time"] + key = f"{file_name}_{spec_id}" + data[key] = [ + file_name, + spec_id, + spec["intensity array"], + spec["m/z array"], + mz_range, + rt, + mass_analyzer.get(instrument_configuration_ref, "unknown"), + fragmentation, + ] + data_iter.close() + @staticmethod def get_file_list(source: Union[str, Path, List[Union[str, Path]]], ext: str = "mzml") -> List[Path]: """ @@ -225,43 +251,48 @@ def _get_scans_pymzml( data_iter = pymzml.run.Reader(file_path, args=args, kwargs=kwargs) file_name = file_path.stem mass_analyzer = get_mass_analyzer(file_path) + namespace = "{http://psi.hupo.org/ms/mzml}" + if scanidx is None: - for spec in data_iter: - if spec.ms_level != 1: # filter out ms1 spectra if there are any - key = f"{file_name}_{spec.ID}" - instrument_configuration_ref = spec["scanList"]["scan"][0].get("instrumentConfigurationRef", "") - filter_string = str(spec.element.find(".//*[@accession='MS:1000512']").get("value")) - fragmentation = filter_string.split("@")[1][:3].upper() - mz_range = filter_string.split("[")[1][:-1] - data[key] = [ - file_name, - spec.ID, - spec.i, - spec.mz, - mz_range, - spec.scan_time_in_minutes(), - mass_analyzer.get(instrument_configuration_ref, "unknown"), - fragmentation, - ] + spectra = data_iter else: - for idx in scanidx: - spec = data_iter[idx] - # this does not work if some spectra are filtered out, e.g. mzML files with only MS2 spectra, see: - # https://github.com/pymzml/pymzML/blob/a883ff0e61fd97465b0a74667233ff594238e335/pymzml/file_classes - # /standardMzml.py#L81-L84 - key = f"{file_name}_{spec.ID}" - instrument_configuration_ref = spec["scanList"]["scan"][0].get("instrumentConfigurationRef", "") - filter_string = str(spec.element.find(".//*[@accession='MS:1000512']").get("value")) - fragmentation = filter_string.split("@")[1][:3].upper() - mz_range = filter_string.split("[")[1][:-1] - data[key] = [ - file_name, - spec.ID, - spec.i, - spec.mz, - mz_range, - spec.scan_time_in_minutes(), - mass_analyzer.get(instrument_configuration_ref, "unknown"), - fragmentation, - ] + # this does not work if some spectra are filtered out, e.g. mzML files with only MS2 spectra, see: + # https://github.com/pymzml/pymzML/blob/a883ff0e61fd97465b0a74667233ff594238e335/pymzml/file_classes + # /standardMzml.py#L81-L84 + spectra = (data_iter[idx] for idx in scanidx) + + for spec in spectra: + if spec.ms_level != 2: + continue # filter out ms1 spectra if there are any + key = f"{file_name}_{spec.ID}" + scan = spec.get_element_by_path(["scanList", "scan"])[0] + instrument_configuration_ref = scan.get("instrumentConfigurationRef", "") + activation = spec.get_element_by_path(["precursorList", "precursor", "activation"])[0] + fragmentation = "unknown" + for cv_param in activation: + name = cv_param.get("name") + if name == "collision energy": + pass + if "beam-type" in name: + fragmentation = "HCD" + break + if "collision-induced dissociation" in name: + fragmentation = "CID" + break + else: + fragmentation = name + scan_window = scan.find(f".//{namespace}scanWindow") + scan_lower_limit = scan_window.find(f'./{namespace}cvParam[@accession="MS:1000501"]').get("value") + scan_upper_limit = scan_window.find(f'./{namespace}cvParam[@accession="MS:1000500"]').get("value") + mz_range = f"{scan_lower_limit}-{scan_upper_limit}" + data[key] = [ + file_name, + spec.ID, + spec.i, + spec.mz, + mz_range, + spec.scan_time_in_minutes(), + mass_analyzer.get(instrument_configuration_ref, "unknown"), + fragmentation, + ] data_iter.close() From 4a60a9ce8c31b5ecacc5a61b5c386765eff58d62 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 24 Oct 2023 09:40:29 +0200 Subject: [PATCH 3/9] added unittests + cleanup for msraw --- .flake8 | 2 +- spectrum_io/raw/msraw.py | 132 ++++++++++++++----------------- tests/unit_tests/data/testdf.pkl | Bin 0 -> 10493 bytes tests/unit_tests/test_msraw.py | 25 ++++-- 4 files changed, 79 insertions(+), 80 deletions(-) create mode 100644 tests/unit_tests/data/testdf.pkl diff --git a/.flake8 b/.flake8 index e9108c3..151e3b8 100644 --- a/.flake8 +++ b/.flake8 @@ -5,7 +5,7 @@ max-line-length = 120 max-complexity = 10 docstring-convention = google per-file-ignores = - tests/*:S101 + tests/*:S101,S301,S403 noxfile.py:DAR101 spectrum_io/raw/thermo_raw.py:S603,S404 spectrum_io/raw/msraw.py:S405,S314 diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index 8dc7a46..7d9e5f4 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -25,7 +25,7 @@ def check_analyzer(mass_analyzers: Dict[str, str]) -> Dict[str, str]: accession = mass_analyzers[elem] if accession in ["MS:1000079", "MS:1000484"]: # fourier transform ion cyclotron, orbitrap mass_analyzers[elem] = "FTMS" - elif accession in ["MS:1000082", "MS:1000264" "MS:1000078"]: # quadrupole ion-trap, ion-trap, linear ion-trap + elif accession in ["MS:1000082", "MS:1000264", "MS:1000078"]: # quadrupole ion-trap, ion-trap, linear ion-trap mass_analyzers[elem] = "ITMS" elif accession in ["MS:1000084"]: # TOF mass_analyzers[elem] = "TOF" @@ -143,22 +143,74 @@ def read_mzml( else: raise AssertionError("Choose either 'pymzml' or 'pyteomics'") - data = pd.DataFrame.from_dict(data, orient="index", columns=MZML_DATA_COLUMNS) data["SCAN_NUMBER"] = pd.to_numeric(data["SCAN_NUMBER"]) return data @staticmethod - def _read_mzml_pymzml(file_list: List[Path], scanidx: Optional[List] = None, *args, **kwargs) -> Dict[str, str]: - data = {} + def _read_mzml_pymzml(file_list: List[Path], scanidx: Optional[List] = None, *args, **kwargs) -> pd.DataFrame: + data_dict = {} with warnings.catch_warnings(): warnings.filterwarnings("ignore", category=ImportWarning) for file_path in file_list: logger.info(f"Reading mzML file: {file_path}") - MSRaw._get_scans_pymzml(file_path, data, scanidx, *args, **kwargs) + data_iter = pymzml.run.Reader(file_path, args=args, kwargs=kwargs) + file_name = file_path.stem + mass_analyzer = get_mass_analyzer(file_path) + namespace = "{http://psi.hupo.org/ms/mzml}" + + if scanidx is None: + spectra = data_iter + else: + # this does not work if some spectra are filtered out, e.g. mzML files with only MS2 spectra, see: + # https://github.com/pymzml/pymzML/blob/a883ff0e61fd97465b0a74667233ff594238e335/pymzml/file_classes + # /standardMzml.py#L81-L84 + spectra = (data_iter[idx] for idx in scanidx) + + for spec in spectra: + if spec.ms_level != 2: + continue # filter out ms1 spectra if there are any + key = f"{file_name}_{spec.ID}" + scan = spec.get_element_by_path(["scanList", "scan"])[0] + instrument_configuration_ref = scan.get("instrumentConfigurationRef", "") + activation = spec.get_element_by_path(["precursorList", "precursor", "activation"])[0] + fragmentation = "unknown" + for cv_param in activation: + name = cv_param.get("name") + if name == "collision energy": + pass + if "beam-type" in name: + fragmentation = "HCD" + break + if "collision-induced dissociation" in name: + fragmentation = "CID" + break + else: + fragmentation = name + scan_window = scan.find(f".//{namespace}scanWindow") + scan_lower_limit = float( + scan_window.find(f'./{namespace}cvParam[@accession="MS:1000501"]').get("value") + ) + scan_upper_limit = float( + scan_window.find(f'./{namespace}cvParam[@accession="MS:1000500"]').get("value") + ) + mz_range = f"{scan_lower_limit}-{scan_upper_limit}" + data_dict[key] = [ + file_name, + spec.ID, + spec.i, + spec.mz, + mz_range, + spec.scan_time_in_minutes(), + mass_analyzer.get(instrument_configuration_ref, "unknown"), + fragmentation, + ] + data_iter.close() + data = pd.DataFrame.from_dict(data_dict, orient="index", columns=MZML_DATA_COLUMNS) + return data @staticmethod def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> Dict[str, str]: - data = {} + data_dict = {} for file_path in file_list: mass_analyzer = get_mass_analyzer(file_path) logger.info(f"Reading mzML file: {file_path}") @@ -188,7 +240,7 @@ def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> Dict[str, st mz_range = f"{scan_lower_limit}-{scan_upper_limit}" rt = spec["scanList"]["scan"][0]["scan start time"] key = f"{file_name}_{spec_id}" - data[key] = [ + data_dict[key] = [ file_name, spec_id, spec["intensity array"], @@ -199,6 +251,8 @@ def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> Dict[str, st fragmentation, ] data_iter.close() + data = pd.DataFrame.from_dict(data_dict, orient="index", columns=MZML_DATA_COLUMNS) + return data @staticmethod def get_file_list(source: Union[str, Path, List[Union[str, Path]]], ext: str = "mzml") -> List[Path]: @@ -232,67 +286,3 @@ def get_file_list(source: Union[str, Path, List[Union[str, Path]]], ext: str = " else: raise TypeError("source can only be a single str or Path or a list of files.") return file_list - - @staticmethod - def _get_scans_pymzml( - file_path: Union[str, Path], data: Dict, scanidx: Optional[List] = None, *args, **kwargs - ) -> None: - """ - Reads mzml and generates a dataframe containing intensities and m/z values. - - :param file_path: path to a single mzml file. - :param data: dictionary to be added to by this function - :param scanidx: optional list of scan numbers to extract. if not specified, all scans will be extracted - :param args: additional positional arguments - :param kwargs: additional keyword arguments - """ - if isinstance(file_path, str): - file_path = Path(file_path) - data_iter = pymzml.run.Reader(file_path, args=args, kwargs=kwargs) - file_name = file_path.stem - mass_analyzer = get_mass_analyzer(file_path) - namespace = "{http://psi.hupo.org/ms/mzml}" - - if scanidx is None: - spectra = data_iter - else: - # this does not work if some spectra are filtered out, e.g. mzML files with only MS2 spectra, see: - # https://github.com/pymzml/pymzML/blob/a883ff0e61fd97465b0a74667233ff594238e335/pymzml/file_classes - # /standardMzml.py#L81-L84 - spectra = (data_iter[idx] for idx in scanidx) - - for spec in spectra: - if spec.ms_level != 2: - continue # filter out ms1 spectra if there are any - key = f"{file_name}_{spec.ID}" - scan = spec.get_element_by_path(["scanList", "scan"])[0] - instrument_configuration_ref = scan.get("instrumentConfigurationRef", "") - activation = spec.get_element_by_path(["precursorList", "precursor", "activation"])[0] - fragmentation = "unknown" - for cv_param in activation: - name = cv_param.get("name") - if name == "collision energy": - pass - if "beam-type" in name: - fragmentation = "HCD" - break - if "collision-induced dissociation" in name: - fragmentation = "CID" - break - else: - fragmentation = name - scan_window = scan.find(f".//{namespace}scanWindow") - scan_lower_limit = scan_window.find(f'./{namespace}cvParam[@accession="MS:1000501"]').get("value") - scan_upper_limit = scan_window.find(f'./{namespace}cvParam[@accession="MS:1000500"]').get("value") - mz_range = f"{scan_lower_limit}-{scan_upper_limit}" - data[key] = [ - file_name, - spec.ID, - spec.i, - spec.mz, - mz_range, - spec.scan_time_in_minutes(), - mass_analyzer.get(instrument_configuration_ref, "unknown"), - fragmentation, - ] - data_iter.close() diff --git a/tests/unit_tests/data/testdf.pkl b/tests/unit_tests/data/testdf.pkl new file mode 100644 index 0000000000000000000000000000000000000000..497ac97b2d938d680a6f53ad3501e0faac3a050f GIT binary patch literal 10493 zcmZ{q2Ut}{7RN^v8}=3}UX3DHu%S_-Fn|paGy-COmj_6ZCPh#z6BHGF8quf5#Bz2XQv(Wyxh 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pd.testing.assert_frame_equal(df, target_df) + + class TestMsraw(unittest.TestCase): """Class to test msraw.""" - def test_read_mzml(self): + def test_read_mzml_with_pyteomics(self): """Test read_mzml.""" - source = Path(__file__).parent / "data/test.mzml" - - msraw_obj = msraw.MSRaw(source, source) - df = msraw_obj.read_mzml(source) + _test_read_mzml(package="pyteomics") - self.assertIsInstance(df, pd.DataFrame) - self.assertEqual(df.shape[1], 8) - self.assertListEqual(list(df.columns), MZML_DATA_COLUMNS) + def test_read_mzml_with_pymzml(self): + """Test read_mzml.""" + _test_read_mzml(package="pymzml") From 398ce26735380d83819f12ad40335e43250834b4 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 24 Oct 2023 09:46:02 +0200 Subject: [PATCH 4/9] fixed return type --- spectrum_io/raw/msraw.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index 7d9e5f4..f2b29cc 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -209,7 +209,7 @@ def _read_mzml_pymzml(file_list: List[Path], scanidx: Optional[List] = None, *ar return data @staticmethod - def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> Dict[str, str]: + def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> pd.DataFrame: data_dict = {} for file_path in file_list: mass_analyzer = get_mass_analyzer(file_path) From ecdf3c1cd90d7a546701992f88cf0673dd361bfd Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 31 Oct 2023 14:46:36 +0100 Subject: [PATCH 5/9] also read collision energy from mzml --- spectrum_io/raw/msraw.py | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index f2b29cc..578aca0 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -174,16 +174,16 @@ def _read_mzml_pymzml(file_list: List[Path], scanidx: Optional[List] = None, *ar instrument_configuration_ref = scan.get("instrumentConfigurationRef", "") activation = spec.get_element_by_path(["precursorList", "precursor", "activation"])[0] fragmentation = "unknown" + collision_energy = 0.0 for cv_param in activation: name = cv_param.get("name") if name == "collision energy": - pass + collision_energy = float(cv_param.get("value")) + continue if "beam-type" in name: fragmentation = "HCD" - break - if "collision-induced dissociation" in name: + elif "collision-induced dissociation" in name: fragmentation = "CID" - break else: fragmentation = name scan_window = scan.find(f".//{namespace}scanWindow") @@ -203,6 +203,7 @@ def _read_mzml_pymzml(file_list: List[Path], scanidx: Optional[List] = None, *ar spec.scan_time_in_minutes(), mass_analyzer.get(instrument_configuration_ref, "unknown"), fragmentation, + collision_energy, ] data_iter.close() data = pd.DataFrame.from_dict(data_dict, orient="index", columns=MZML_DATA_COLUMNS) @@ -224,15 +225,14 @@ def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> pd.DataFrame instrument_configuration_ref = scan.get("instrumentConfigurationRef", "") activation = spec["precursorList"]["precursor"][0]["activation"] fragmentation = "unknown" - for key in activation.keys(): + collision_energy = 0.0 + for key, value in activation.items(): if key == "collision energy": - pass - if "beam-type" in key: + collision_energy = value + elif "beam-type" in key: fragmentation = "HCD" - break - if "collision-induced dissociation" in key: + elif "collision-induced dissociation" in key: fragmentation = "CID" - break else: fragmentation = key scan_lower_limit = scan["scanWindowList"]["scanWindow"][0]["scan window lower limit"] @@ -249,6 +249,7 @@ def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> pd.DataFrame rt, mass_analyzer.get(instrument_configuration_ref, "unknown"), fragmentation, + collision_energy, ] data_iter.close() data = pd.DataFrame.from_dict(data_dict, orient="index", columns=MZML_DATA_COLUMNS) From 96a67d17d24ec5264c82128b8a7aa51966dffe59 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 31 Oct 2023 23:19:57 +0100 Subject: [PATCH 6/9] added a workaround for misisng collision column --- spectrum_io/raw/msraw.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index 578aca0..a9ba15b 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -136,6 +136,10 @@ def read_mzml( """ file_list = MSRaw.get_file_list(source, ext) + # this is a temporary fix until this is changed in spectrum_fundamentals + global MZML_DATA_COLUMNS + MZML_DATA_COLUMNS = MZML_DATA_COLUMNS + ["COLLISION_ENERGY"] + if package == "pymzml": data = MSRaw._read_mzml_pymzml(file_list, scanidx, *args, **kwargs) elif package == "pyteomics": From 550b66919306824f8c04a38b1bd2ad6ce60f9f21 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Fri, 10 Nov 2023 16:05:51 +0100 Subject: [PATCH 7/9] remove temporary fix --- spectrum_io/raw/msraw.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index a9ba15b..578aca0 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -136,10 +136,6 @@ def read_mzml( """ file_list = MSRaw.get_file_list(source, ext) - # this is a temporary fix until this is changed in spectrum_fundamentals - global MZML_DATA_COLUMNS - MZML_DATA_COLUMNS = MZML_DATA_COLUMNS + ["COLLISION_ENERGY"] - if package == "pymzml": data = MSRaw._read_mzml_pymzml(file_list, scanidx, *args, **kwargs) elif package == "pyteomics": From f19dd9b402dd8f5632e3f5f7ddd64c5b531fcaa6 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Fri, 10 Nov 2023 16:06:08 +0100 Subject: [PATCH 8/9] new version containing COLLISION_ENERGY column --- tests/unit_tests/data/testdf.pkl | Bin 10493 -> 10528 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/tests/unit_tests/data/testdf.pkl b/tests/unit_tests/data/testdf.pkl index 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[tool.poetry.dev-dependencies] pytest = ">=6.2.3"