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.. code-block:: python
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import pymzml
def main():
"""
Compare multiple spectra and return the cosine distance between them.
The returned value is between 0 and 1, a returned value of 1
represents highest similarity.
usage:
./compare_spectra.py
"""
example_file = os.path.join(
os.path.dirname(__file__), os.pardir, "tests", "data", "example.mzML"
)
print(
"""
Comparing spectra
"""
)
# print(example_file)
run = pymzml.run.Reader(example_file)
tmp = []
for spec in run:
if spec.ms_level == 1:
print("Parsing spectrum lvl 1 has id {0}".format(spec.ID))
tmp.append(spec)
if len(tmp) >= 3:
break
print("Print total number of specs collected {0}".format(len(tmp)))
for compare_tuples in [(0, 1), (0, 2), (1, 2)]:
print(
"Cosine between spectra {0} & {1} is {2:1.4f}".format(
compare_tuples[0] + 1,
compare_tuples[1] + 1,
tmp[compare_tuples[0]].similarity_to(tmp[compare_tuples[1]]),
)
)
print(
"Cosine score between first spectrum against itself: {0:1.4f}".format(
tmp[0].similarity_to(tmp[0])
)
)
if __name__ == "__main__":
main()
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