Skip to content

Support pyopenms 3.6 API #86

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ypriverol merged 1 commit into from
Oct 9, 2026
Merged

Support pyopenms 3.6 API #86

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 18 additions & 4 deletions quantmsutils/mzml/ms1_feature_finder.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@
logging.basicConfig(format="%(asctime)s [%(funcName)s] - %(message)s", level=logging.INFO)
logger = logging.getLogger(__name__)

_PYOPENMS_VERSION = tuple(int(p) for p in oms.__version__.split(".")[:2])


class MS1FeatureDetector:
"""
Expand All @@ -51,6 +53,21 @@ def __init__(self, ms_level: int = 1):
self.options = oms.PeakFileOptions()
self.options.setMSLevels([self.ms_level])

@staticmethod
def _pick_experiment(
picker: oms.PeakPickerHiRes, experiment: oms.MSExperiment
) -> oms.MSExperiment:
"""Centroid an experiment, supporting both pyopenms peak-picker APIs.

pyopenms >= 3.6 returns the picked experiment; older versions fill an
output experiment passed by reference.
"""
if _PYOPENMS_VERSION >= (3, 6):
return picker.pickExperiment(experiment, False)
picked = oms.MSExperiment()
picker.pickExperiment(experiment, picked, False)
return picked

def _calc_tic(self, experiment: oms.MSExperiment) -> float:
"""
Calculate all the TIC in the MS experiment, summing all intensities from all scans.
Expand Down Expand Up @@ -249,12 +266,9 @@ def process_file(
experiment = oms.MSExperiment()
picker = oms.PeakPickerHiRes()

filtered_experiment = oms.MSExperiment()

file_handler.setOptions(self.options)
file_handler.load(str(input_path), experiment)
picker.pickExperiment(experiment, filtered_experiment, False)
experiment = filtered_experiment
experiment = self._pick_experiment(picker, experiment)

filtered_experiment = oms.MSExperiment()
for spec in experiment:
Expand Down
8 changes: 5 additions & 3 deletions quantmsutils/psm/psm_conversion.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,9 +103,11 @@ def convert_psm(
else:
search_engines = [prot_ids[0].getSearchEngine()]

reference_file_name = os.path.splitext(
prot_ids[0].getMetaValue("spectra_data")[0].decode("UTF-8")
)[0]
spectra_data = prot_ids[0].getMetaValue("spectra_data")[0]
# pyopenms < 3.6 returns bytes here, >= 3.6 returns str
if isinstance(spectra_data, bytes):
spectra_data = spectra_data.decode("UTF-8")
reference_file_name = os.path.splitext(spectra_data)[0]
spectra_df = pd.read_parquet(ms2_file) if ms2_file else None

if spectra_df is not None:
Expand Down