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import sys
import os
import unittest
sys.path.append(os.path.abspath("."))
import pymzml
from pymzml.spec import PROTON
import pymzml.run as run
import test_file_paths
import numpy as np
class SpectrumMS2Test(unittest.TestCase):
"""
BSA test file
Peptide @
Scan: 2548
RT [min] 28.96722412109367
Selected_precursor [(443.711242675781, 0.0)]
"""
def setUp(self):
""" """
# self.paths = [
# os.path.join( DATA_FOLDER, file ) for file in DATA_FILES]
self.paths = test_file_paths.paths
path = self.paths[9]
self.Run = run.Reader(path)
self.spec = self.Run[2548]
def test_scan_time(self):
scan_time = self.spec.scan_time_in_minutes()
scan_time2 = self.spec.scan_time_in_minutes()
self.assertIsNotNone(scan_time)
self.assertIsInstance(scan_time, float)
self.assertEqual(round(scan_time, 4), round(28.96722412109367, 4))
self.assertEqual(scan_time, scan_time2)
def test_select_precursors(self):
selected_precursor = self.spec.selected_precursors
self.assertIsInstance(selected_precursor[0], dict)
self.assertIsInstance(selected_precursor[0]["mz"], float)
self.assertIsInstance(selected_precursor[0]["i"], float)
self.assertIsInstance(selected_precursor[0]["charge"], int)
assert selected_precursor[0]["mz"] == 443.711242675781
assert selected_precursor[0]["i"] == 0.0
assert selected_precursor[0]["precursor id"] is None
def test_ion_mode(self):
assert self.spec["positive scan"] is True
def test_ion_mode_non_existent(self):
assert self.spec["negative scan"] is None
@unittest.skipIf(pymzml.spec.DECON_DEP is False, "ms_deisotope was not installed")
def test_deconvolute_peaks(self):
charge = 3
test_mz = 430.313
arr = np.array([(test_mz, 100), (test_mz + PROTON / charge, 49)])
spec = self.Run[2548]
spec.set_peaks(arr, "centroided")
decon = spec.peaks("deconvoluted")
self.assertEqual(len(decon), 1)
decon_mz = (test_mz * charge) - charge * PROTON
self.assertEqual(decon[0][0], decon_mz)
self.assertEqual(decon[0][1], 149) # 149 since itensities are 100 and 49
self.assertEqual(decon[0][2], 3)
def test_remove_precursor_peak(self):
# breakpoint()
# breakpoint()
test_mz = 443.71124268 # precursor peak
self.spec.set_peaks(np.array([(test_mz, 200)]), "centroided")
self.spec.set_peaks(np.array([(test_mz, 200)]), "raw")
assert self.spec.has_peak(test_mz)
self.spec._transformed_mz_with_error = None
new_peaks = self.spec.remove_precursor_peak()
found_peaks = self.spec.has_peak(test_mz)
assert len(found_peaks) == 0
if __name__ == "__main__":
unittest.main(verbosity=3)
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