Source code for simple_parser

#!/usr/bin/env python
import sys
import pymzml

[docs]def main(mzml_file): ''' Basic example script to demonstrate the usage of pymzML. Requires a mzML file as first argument. usage: ./simple_parser.py <path_to_mzml_file> Note: This script uses the new syntax with the MS level being a property of the spectrum class ( Spectrum.ms_level ). The old syntax can be found in the script simple_parser_v2.py where the MS level can be queried as a key (Spectrum['ms level']) ''' run = pymzml.run.Reader(mzml_file) for n, spec in enumerate( run ): print( 'Spectrum {0}, MS level {ms_level} @ RT {scan_time:1.2f}'.format( spec.ID, ms_level = spec.ms_level, scan_time = spec.scan_time_in_minutes() ) ) print( 'Parsed {0} spectra from file {1}'.format( n, mzml_file ) ) print()
if __name__ == '__main__': if len(sys.argv) < 2: print(main.__doc__) exit() mzml_file = sys.argv[1] main(mzml_file)