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#!/usr/bin/env python
import pymzml
from collections import defaultdict as ddict
import os
def main():
"""
Testscript to isolate the n-highest peaks from an example file.
Usage:
./highest_peaks.py
Parses the file '../tests/data/example.mzML' and extracts the 2 highest
intensities from each spectrum.
"""
example_file = os.path.join(
os.path.dirname(__file__), os.pardir, "tests", "data", "example.mzML"
)
run = pymzml.run.Reader(example_file)
highest_i_dict = ddict(list)
number_of_peaks_to_extract = 2
for spectrum in run:
# print( spectrum.ID )
if spectrum.ms_level == 1:
for mz, i in spectrum.highest_peaks(number_of_peaks_to_extract):
highest_i_dict[spectrum.ID].append(i)
for spectrum_id, highest_peak_list in highest_i_dict.items():
assert len(highest_peak_list) == number_of_peaks_to_extract
print(
"Spectrum {0}; highest intensities: {1}".format(
spectrum_id, highest_peak_list
)
)
if __name__ == "__main__":
main()
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