Source code for matchms.importing.load_from_mgf

from typing import Generator, TextIO, Union
import numpy
from pyteomics.mgf import MGF
from ..Spectrum import Spectrum

[docs]def load_from_mgf(source: Union[str, TextIO], metadata_harmonization: bool = True) -> Generator[Spectrum, None, None]: """Load spectrum(s) from mgf file. This function will create ~matchms.Spectrum for every spectrum in the given .mgf file (or the file-like object). Examples: .. code-block:: python from matchms.importing import load_from_mgf file_mgf = "pesticides.mgf" spectra_from_path = list(load_from_mgf(file_mgf)) # Or you can read the file in your application with open(file_mgf, 'r') as spectra_file: spectra_from_file = list(load_from_mgf(spectra_file)) Parameters ---------- source: Accepts both filename (with path) for .mgf file or a file-like object from a preloaded MGF file. metadata_harmonization : bool, optional Set to False if metadata harmonization to default keys is not desired. The default is True. """ for pyteomics_spectrum in MGF(source, convert_arrays=1): metadata = pyteomics_spectrum.get("params", None) mz = pyteomics_spectrum["m/z array"] intensities = pyteomics_spectrum["intensity array"] # Sort by mz (if not sorted already) if not numpy.all(mz[:-1] <= mz[1:]): idx_sorted = numpy.argsort(mz) mz = mz[idx_sorted] intensities = intensities[idx_sorted] yield Spectrum(mz=mz, intensities=intensities, metadata=metadata, metadata_harmonization=metadata_harmonization)