from pathlib import Path
from typing import Generator, Union
import numpy as np
from pyteomics.mzml import read
from matchms.importing.parsing_utils import parse_mzml_mzxml_metadata, sort_by_mz
from matchms.Spectrum import Spectrum
[docs]
def load_from_mzml(
filename: Union[str, Path], ms_level: int = 2, metadata_harmonization: bool = True
) -> Generator[Spectrum, None, None]:
"""Load spectrum(s) from mzml file.
This function will create ~matchms.Spectrum for every spectrum of desired
ms_level found in a given MzML file. For more extensive parsing options consider
using pyteomics or pymzml packages.
Example:
.. code-block:: python
from matchms.importing import load_from_mzml
file_mzml = "testdata.mzml"
spectra = list(load_from_mzml(file_mzml))
Parameters
----------
filename:
Filename for mzml file to import.
ms_level:
Specify which ms level to import. Default is 2.
metadata_harmonization : bool, optional
Set to False if metadata harmonization to default keys is not desired.
The default is True.
"""
if isinstance(filename, Path):
filename = str(filename) # pyteomics does not support pathlib.Path
with read(filename, dtype=dict) as reader:
for pyteomics_spectrum in reader:
if "ms level" in pyteomics_spectrum and pyteomics_spectrum["ms level"] == ms_level:
metadata = parse_mzml_mzxml_metadata(pyteomics_spectrum)
mz = np.asarray(pyteomics_spectrum["m/z array"], dtype="float")
intensities = np.asarray(pyteomics_spectrum["intensity array"], dtype="float")
mz, intensities = sort_by_mz(mz=mz, intensities=intensities)
yield Spectrum(
mz=mz, intensities=intensities, metadata=metadata, metadata_harmonization=metadata_harmonization
)