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