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)