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import unittest,os,copy
import env
import pyopenms
from collections import defaultdict
eps = 2
class TestSILACAnalyzer(unittest.TestCase):
"""Emulates the behavior of SILACAnalyzer"""
def setUp(self):
self.testdirname = os.path.join(env.OPEN_MS_SRC, "source/TEST/TOPP")
# set up files
self.infile = os.path.join(self.testdirname, "SILACAnalyzer.mzML")
def test_run_SILACAnalyzer(self):
exp = pyopenms.MSExperiment()
out_map = pyopenms.ConsensusMap()
pyopenms.FileHandler().loadExperiment(self.infile, exp)
exp.updateRanges()
#
# 1. filter MS1 level (only keep MS1)
#
tmp = copy.copy(exp)
for spectrum in exp:
if spectrum.getMSLevel() == 1:
tmp.addSpectrum(spectrum)
exp = tmp
exp.sortSpectra(True)
selected_labels = "Lys8"
charge_min = 2
charge_max = 2
missed_cleavages = 0
isotopes_per_peptide_min = 3
isotopes_per_peptide_max = 3
rt_threshold = 80
rt_min = 0
intensity_cutoff = 10
intensity_correlation = 0.95
model_deviation = 10
allow_missing_peaks = False
label_identifiers = {"Lys8" : 8.0141988132}
#
# 2. set parameters
#
analyzer = pyopenms.SILACAnalyzer()
analyzer.initialize(
# section sample
selected_labels,
charge_min,
charge_max,
missed_cleavages,
isotopes_per_peptide_min,
isotopes_per_peptide_max,
# section "algorithm"
rt_threshold,
rt_min,
intensity_cutoff,
intensity_correlation,
model_deviation,
allow_missing_peaks,
# labels
label_identifiers)
#
# 3. run
#
analyzer.run_all(exp, out_map)
out_map.sortByPosition()
self.assertEqual(out_map.size(), 3)
self.assertEqual(out_map[0].getQuality(), 8.0)
self.assertEqual(out_map[1].getQuality(), 8.0)
self.assertEqual(out_map[2].getQuality(), 8.0)
self.assertAlmostEqual(out_map[0].getRT(), 6632.409179688, eps)
self.assertAlmostEqual(out_map[1].getRT(), 6635.169433594, eps)
self.assertAlmostEqual(out_map[2].getRT(), 6657.56445312, eps)
self.assertAlmostEqual(out_map[0].getMZ(), 668.321350097656, eps)
self.assertAlmostEqual(out_map[1].getMZ(), 670.894470214844, eps)
self.assertAlmostEqual(out_map[2].getMZ(), 668.8262329102, eps)
if __name__ == '__main__':
unittest.main()
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