Source code for simple_parser_v2

#!/usr/bin/env python
import sys
import pymzml
from collections import defaultdict as ddict


[docs]def main(mzml_file): ''' Basic example script to demonstrate the usage of pymzML. Requires a mzML file as first argument. usage: ./simple_parser_v2.py <path_to_mzml_file> Note: This script uses the old syntax where the MS level can be queried as a key (Spectrum['ms level']). The current syntax can be found in simple_parser.py ''' run = pymzml.run.Reader(mzml_file) # print( run[10000].keys() ) stats = ddict(int) for n, spec in enumerate( run ): print( 'Spectrum {0}, MS level {ms_level}'.format( n, ms_level = spec['ms level'] ), end = '\r' ) # the old method to obtain peaks from the Spectrum class stats[spec.ID] = len(spec.centroidedPeaks) print( 'Parsed {0} spectra from file {1}'.format( len(stats.keys()), mzml_file, ) ) print()
if __name__ == '__main__': if len(sys.argv) < 2: print(main.__doc__) exit() mzml_file = sys.argv[1] main(mzml_file)