def test_weird_summing_mgf(self):
path = "tests/data/weird_sum.mgf"
output = "/home/tobiass/weird_sum.csv"
output_mgf = "tests/data/temp/weird_mgf.mgf"
ma = MgfAnnotater(path, output)
ma.load_msconvert_mgf()
ma.export_annotated_spectra_to_mgf(output_mgf)
ms = MasterSpectrum()
ms.load_from_mgf("tests/data/temp/weird_mgf.mgf", ignoreCharges=True)
assert_equal(round(ms.spectrum[0][179][0].intensity, 4), round(0.0025, 4))
def test_patch_mgf(self):
ms = MasterSpectrum()
ms.load_from_mgf(
'tests/data/cetsa_101287_A01_P013190_S00_N01_R1_TMT10_3spectra_shorted.mgf',
ignoreCharges=True)
assert_equal(177 in ms.spectrum[0].keys(), True)
mgfP = MgfPatcher(delta_func=calculate_Delta_by_ppm(20))
mgfP.readExclusionList('tests/data/exclusionList.txt')
mgfP.patchMgf(
'tests/data/cetsa_101287_A01_P013190_S00_N01_R1_TMT10_3spectra_shorted.mgf',
'tests/data/temp/cetsa_101287_A01_P013190_S00_N01_R1_TMT10_3spectra_shorted_patched.mgf'
)
ms = MasterSpectrum()
ms.load_from_mgf(
'tests/data/temp/cetsa_101287_A01_P013190_S00_N01_R1_TMT10_3spectra_shorted_patched.mgf',
ignoreCharges=True)
assert_equal(177 in ms.spectrum[0].keys(), False)
assert_equal(433 in ms.spectrum[0].keys(), False)
