Source code for get_precursors
#!/usr/bin/env python
import os
from operator import itemgetter
import pymzml
[docs]def main():
"""
Extract the 10 most often fragmented precursors from the BSA example file.
This can e.g. be used for defining exclusion lists for further MS runs.
usage:
./get_precursors.py
"""
example_file = os.path.join(
os.path.dirname(__file__),
os.pardir,
'tests',
'data',
'BSA1.mzML.gz'
)
run = pymzml.run.Reader(example_file)
fragmented_precursors = {}
for spectrum in run:
if spectrum.ms_level == 2:
selected_precursors = spectrum.selected_precursors
if spectrum.selected_precursors is not None:
for precursor_dict in selected_precursors:
precursor_mz = precursor_dict['mz']
precursor_i = precursor_dict['i']
rounded_precursor_mz = round(precursor_mz,3)
if rounded_precursor_mz not in fragmented_precursors.keys():
fragmented_precursors[rounded_precursor_mz] = []
fragmented_precursors[rounded_precursor_mz].append(spectrum.ID)
precursor_info_list = []
for rounded_precursor_mz, spectra_list in fragmented_precursors.items():
precursor_info_list.append(
(
len(spectra_list),
rounded_precursor_mz,
spectra_list
)
)
for pos, (number_of_spectra, rounded_precursor_mz, spectra_list) in enumerate(sorted(precursor_info_list, reverse=True)):
print(
'Found precursor: {0} in spectra: {1}'.format(
rounded_precursor_mz,
spectra_list
)
)
if pos > 8:
break
if __name__ == '__main__':
main()