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#!/usr/bin/env python
import os
import pymzml
def main():
"""
Demonstration of the extraction of a specific ion chromatogram, i.e. XIC or EIC
All intensities and m/z values for a target m/z are extracted.
usage:
./extract_ion_chromatogram.py
"""
example_file = os.path.join(
os.path.dirname(__file__), os.pardir, "tests", "data", "example.mzML"
)
run = pymzml.run.Reader(example_file)
time_dependent_intensities = []
MZ_2_FOLLOW = 70.06575775
for spectrum in run:
if spectrum.ms_level == 1:
has_peak_matches = spectrum.has_peak(MZ_2_FOLLOW)
if has_peak_matches != []:
for mz, I in has_peak_matches:
time_dependent_intensities.append(
[spectrum.scan_time_in_minutes(), I, mz]
)
print("RT \ti \tmz")
for rt, i, mz in time_dependent_intensities:
print("{0:5.3f}\t{1:13.4f}\t{2:10}".format(rt, i, mz))
return
if __name__ == "__main__":
main()
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