"""Read MS2 spectra."""
from __future__ import annotations
from collections.abc import Generator
from pathlib import Path
import numpy as np
from ms2rescore_rs import get_ms2_spectra # type: ignore[ty:unresolved-import]
import ms2pip.exceptions as exceptions
from ms2pip.spectrum import ObservedSpectrum
[docs]
def read_spectrum_file(spectrum_file: str) -> Generator[ObservedSpectrum, None, None]:
"""
Read MS2 spectra from a supported file format; inferring the type from the filename extension.
Parameters
----------
spectrum_file
Path to MGF or mzML file.
Yields
------
ObservedSpectrum
Raises
------
UnsupportedSpectrumFiletypeError
If the file extension is not supported.
"""
try:
spectra = get_ms2_spectra(str(spectrum_file))
except ValueError as e:
raise exceptions.UnsupportedSpectrumFiletypeError(Path(spectrum_file).suffixes) from e
for spectrum in spectra:
obs_spectrum = ObservedSpectrum(
mz=np.array(spectrum.mz, dtype=np.float32),
intensity=np.array(spectrum.intensity, dtype=np.float32),
identifier=str(spectrum.identifier),
precursor_mz=float(spectrum.precursor.mz),
precursor_charge=int(spectrum.precursor.charge),
retention_time=float(spectrum.precursor.rt),
)
# Workaround for mobiusklein/mzdata#3
if (
obs_spectrum.identifier == ""
or obs_spectrum.mz.shape[0] == 0
or obs_spectrum.intensity.shape[0] == 0
):
continue
yield obs_spectrum