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#!/usr/bin/env python3.2
# -*- coding: utf-8 -*-
# encoding: utf-8
#
# pymzml
#
# Copyright (C) 2014 T. Bald, J. Barth, M. Specht, C. Fufezan, H. Roest
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import sys
import unittest
import pymzml
sys.path.append('example_scripts')
import get_example_file
class TestDeconvolution(unittest.TestCase):
def setUp(self):
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 spec in run:
# there is only one spectrum, so just read this
self.spec = spec
break
def check_peaklist(self, mz_range, result):
tmp = self.spec.deRef()
deconvoluted_peak_list = tmp.deconvolutedPeaks
# reduce to interesting range
tmp_deconv_peaks = [ (mass,i) for mass, i in deconvoluted_peak_list if mz_range[0] <= mass <= mz_range[1] ]
self.assertEqual(len(tmp_deconv_peaks), len(result))
for pos, (mass, i) in enumerate(tmp_deconv_peaks):
self.assertAlmostEqual(mass, result[pos][0])
self.assertAlmostEqual(i, result[pos][1])
def check_deconvolution_with_debug_parameter(self, mz_range, expected_result):
tmp = self.spec.deRef()
deconv_peaklist, masses2mz = tmp.deconvolute_peaks(debug = True)
result = []
for mass, results in masses2mz.items():
if mz_range[0] < mass < mz_range[1]:
result.append([mass, results])
self.assertEqual(result, expected_result)
def check_devonvolution_intensities(self, mz_range, expected_result):
tmp = self.spec.deRef()
tmp.reduce(tuple(mz_range))
self.assertEqual(tmp._get_deisotopedMZ_for_chargeDeconvolution(), expected_result)
def test_masses(self):
self.check_peaklist((1163, 1208), [(1190.5785115257675, 19276.015691004373)])
# this is correct
self.check_peaklist((1191, 1400), [(1208.5995290987673, 27546.527600749054)])
self.check_peaklist((2300, 2500), [(2395.169033526201, 19792.568515412233)])
def test_devonvolution_intensities(self):
# belonging to mass 1190
self.check_devonvolution_intensities([590, 615], [(596.2956063083736, 9214.135922430825, 2, 2), (605.3046530030003, 14551.997036341349, 2, 3)])
# belonging to mass 1190
self.check_devonvolution_intensities([1190, 1204], [(1191.5876398350977, 10061.879768573546, 1, 3), (1198.5917932298705, 19792.568515412233, 2, 4)])
def test_deconvolution_with_debug_parameter(self):
expected_result = [[1208.5947530724607, [(605.3046530030003, 14551.997036341349, 2, 3)]],
[1208.604305125074, [(1209.611581591844, 12994.530564407705, 1, 3)]]]
self.check_deconvolution_with_debug_parameter([1208, 1210], expected_result)
expected_result = [[2395.169033526201, [(1198.5917932298705, 19792.568515412233, 2, 4)]]]
self.check_deconvolution_with_debug_parameter([2390, 2400], expected_result)
expected_result = [[1190.5803633683277, [(1191.5876398350977, 10061.879768573546, 1, 3)]],
[1190.5766596832073, [(596.2956063083736, 9214.135922430825, 2, 2)]]]
self.check_deconvolution_with_debug_parameter([1163, 1208], expected_result)
if __name__ == '__main__':
unittest.main()
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