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


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)