Source code for highest_peaks
#!/usr/bin/env python
import pymzml
from collections import defaultdict as ddict
import os
[docs]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()