# Source code for get_precursors

    #!/usr/bin/env python

    from __future__ import print_function
    import pymzml
    import os
    from operator import itemgetter

    def main():
        """
        Extract the 10 most often fragmented precursors from the BSA example file.

        This can e.g. be used for defining exclusion lists for further MS runs.

        usage:

            ./get_precursors.py

        """

        example_file = os.path.join(
            os.path.dirname(__file__),
            os.pardir,
            'tests',
            'data',
            'BSA1.mzML.gz'
        )
        run = pymzml.run.Reader(example_file)
        fragmented_precursors = {}
        for spectrum in run:
            if spectrum.ms_level == 2:
                selected_precursors = spectrum.selected_precursors
                if spectrum.selected_precursors is not None:
                    for precursor_mz, precursor_intensity in selected_precursors:
                        rounded_precursor_mz = round(precursor_mz,3)
                        if rounded_precursor_mz not in fragmented_precursors.keys():
                            fragmented_precursors[rounded_precursor_mz] = []
                        fragmented_precursors[rounded_precursor_mz].append(spectrum.ID)

        precursor_info_list = []
        for rounded_precursor_mz, spectra_list in fragmented_precursors.items():
            precursor_info_list.append(
                (
                    len(spectra_list),
                    rounded_precursor_mz,
                    spectra_list
                )
            )

        for pos, (number_of_spectra, rounded_precursor_mz, spectra_list) in enumerate(sorted(precursor_info_list, reverse=True)):
            print(
                'Found precursor: {0} in spectra: {1}'.format(
                    rounded_precursor_mz,
                    spectra_list
                )
            )
            if pos > 8:
                break

    if __name__ == '__main__':
        main()