# Source code for extract_ion_chromatogram

    #!/usr/bin/env python

    from __future__ import print_function
    import sys
    import pymzml
    import os

    def main():
        """
        Demonstration of the extraction of a specific ion chromatogram, i.e. XIC or EIC

        All intensities and m/z vlaues for a target m/z are extracted.

        usage:

            ./extract_ion_chromatogram.py

        """

        example_file = os.path.join(
            os.path.dirname(__file__),
            os.pardir,
            'tests',
            'data',
            'example.mzML'
        )
        run = pymzml.run.Reader(
            example_file
        )
        time_dependent_intensities = []

        MZ_2_FOLLOW = 70.06575775

        for spectrum in run:
            if spectrum.ms_level == 1:
                has_peak_matches = spectrum.has_peak( MZ_2_FOLLOW )
                if has_peak_matches != []:
                    for mz,I in has_peak_matches:
                        time_dependent_intensities.append(
                            [
                                spectrum.scan_time_in_minutes(),
                                I,
                                mz
                            ]
                        )
        print('RT   \ti   \tmz')
        for rt, i, mz in time_dependent_intensities:
            print(
                '{0:5.3f}\t{1:13.4f}\t{2:10}'.format(
                    rt,
                    i,
                    mz
                )
            )
        return

    if __name__ == '__main__':
        main()