Source code for highest_peaks

#!/usr/bin/env python

import pymzml
from collections import defaultdict as ddict
import os


[docs]def main(): """ Testscript to isolate the n-highest peaks from an example file. Usage: ./highest_peaks.py Parses the file '../tests/data/example.mzML' and extracts the 2 highest intensities from each spectrum. """ example_file = os.path.join( os.path.dirname(__file__), os.pardir, 'tests', 'data', 'example.mzML' ) run = pymzml.run.Reader( example_file ) highest_i_dict = ddict(list) number_of_peaks_to_extract = 2 for spectrum in run: # print( spectrum.ID ) if spectrum.ms_level == 1: for mz, i in spectrum.highest_peaks(number_of_peaks_to_extract): highest_i_dict[ spectrum.ID ].append(i) for spectrum_id, highest_peak_list in highest_i_dict.items(): assert len(highest_peak_list) == number_of_peaks_to_extract print( 'Spectrum {0}; highest intensities: {1}'.format( spectrum_id, highest_peak_list ) )
if __name__ == '__main__': main()