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#!/usr/bin/env python3.2
"""
Testscript to demonstrate functionality of function :py:func:`spec.Spectrum.hasPeak`
or :py:func:`spec.Spectrum.hasDeconvolutedPeak`
Example:
>>> import pymzml, get_example_file
>>> example_file = get_example_file.open_example('deconvolution.mzml.gz')
>>> run = pymzml.run.Reader(example_file, MS1_Precision = 5e-6, MSn_Precision = 20e-6)
>>> for spectrum in run:
... if spectrum["ms level"] == 2:
... peak_to_find = spectrum.haspeak(1016.5404)
... print(peak_to_find)
(1016.5404, 19141.735187697403)
"""
from __future__ import print_function
import sys
import pymzml
import get_example_file
def main(verbose = False):
example_file = get_example_file.open_example('deconvolution.mzML.gz')
run = pymzml.run.Reader(example_file, MS1_Precision = 5e-6, MSn_Precision = 20e-6)
for spectrum in run:
if verbose:
print("Processing spectrum #{0}".format(spectrum['id']), end="\r")
print('')
if spectrum['ms level'] == 2:
test1 = spectrum.hasDeconvolutedPeak(1044.559675129575)
test2 = spectrum.hasDeconvolutedPeak(1044.5804)
test3 = spectrum.hasDeconvolutedPeak(1044.5806)
test4 = spectrum.hasDeconvolutedPeak(1044.5800)
test5 = spectrum.hasDeconvolutedPeak(6000)
test6 = spectrum.hasPeak(1016.5402567492666)
test7 = spectrum.hasPeak(6000)
tests = [False, False, False, False, False, False, False]
if test1 == [(1044.559675129575, 3809.4356300564586)]:
tests[0] = True
if test2 == [(1044.559675129575, 3809.4356300564586)]:
tests[1] = True
if test3 == []:
tests[2] = True
if test4 == [(1044.559675129575, 3809.4356300564586)]:
tests[3] = True
if test5 == []:
tests[4] = True
if test6 == [(1016.5402567492666, 19141.735187697403)]:
tests[5] = True
if test7 == []:
tests[6] = True
all = True
for i in range(len(tests)):
if not tests[i]:
all = False
if all:
if verbose:
print('All tests were successful.')
else:
print(tests)
if verbose:
print('deconvoluted peaks list:')
print('')
print('centroided peaks list:')
print(spectrum.centroidedPeaks)
print('')
print('deconvolutedPeaks list:')
print(spectrum.deconvolutedPeaks)
print('')
print("1044.559675129575 in deconvoluted spectrum? (should be)", test1)
print("1044.559675129575 + 20 ppm = 1044.5804 in deconvoluted spectrum? (should be)", test2)
print("1044.559675129575 + >20 ppm = 1044.5806 in deconvoluted spectrum? (shouldn't)", test3)
print("1044.5800 in deconvoluted spectrum? (should be)", test4)
print("6000 in deconvoluted spectrum (shouldn't)?", test5)
print("1016.5402567492666 in centroided peaks (True)", test6)
print("6000 in centroided peaks (None)", test7)
if all:
return True
if __name__ == '__main__':
if len(sys.argv) == 2:
if sys.argv[1] == '-v':
main(True)
else:
main()
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