Source code for matchms.importing.load_from_mgf

from typing import Generator, TextIO, Union
from pyteomics.mgf import MGF
from matchms.importing.parsing_utils import parse_spectrum_dict
from matchms.Spectrum import Spectrum

[docs]def load_from_mgf(filename: 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 ---------- filename: 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. """ with MGF(filename, convert_arrays=1) as reader: for pyteomics_spectrum in reader: yield parse_spectrum_dict( spectrum=pyteomics_spectrum, metadata_harmonization=metadata_harmonization)