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#!/usr/bin/env python
import sys
import pymzml
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'])
"""
i = 0
run = pymzml.run.Reader(mzml_file)
for n, spec in enumerate(run):
print(
"Spectrum {0}, MS level {ms_level}".format(
spec["id"],
ms_level=spec["ms level"],
# scan_time = spec['scan_time']
),
end="\r",
)
i = sum(spec.i)
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)
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