def test_peak_parsing(self):
# Spectrum 1
peaks = [(65.0388, 454422.7),
(105.0703, 3594629.8),
(115.0544, 916283.5),
(121.0287, 482029.8),
(139.0544, 904286),
(163.0549, 764499.2),
(164.0627, 2677649.4),
(165.0706, 293933491.2),
(166.0782, 235412982.7),
(183.0812, 3256920.2),
(193.0767, 1661789.6),
(199.0315, 5538869.4),
(201.0474, 7384944.1)]
spec = MBSpectrum(os.path.join(os.path.dirname(__file__), "example_massbank_records", "EQ308406.txt"))
self.assertEqual(peaks, spec.get_peaks())
# Spectrum 2
peaks = [
(116.050500, 2998.000000),
(117.054700, 236.000000),
(118.029100, 170.000000),
(131.037600, 1.23552e13),
(132.045500, 1241.000000),
(133.048300, 116.000000),
(159.032400, 1732.000000),
(160.040200, 10392.000000),
(161.043200, 1399.000000)]
spec = MBSpectrum(os.path.join(os.path.dirname(__file__), "example_massbank_records", "FIO00665.txt"))
self.assertEqual(peaks, spec.get_peaks())
def test_to_sirius(self):
# Spectrum 1 -------------------
spec = MBSpectrum(os.path.join(os.path.dirname(__file__), "example_massbank_records", "FIO00665.txt"))
out = spec.to_sirius_format()
self.assertIn("FIO00665.ms", out)
self.assertIn("FIO00665.tsv", out)
self.assertIsNone(out["FIO00665.tsv"])
self.assertIn(">profile qtof", out["FIO00665.ms"])
# check fragmentation peaks
tmp = out["FIO00665.ms"].split("\n")
for idx, _peak in enumerate(spec.get_peaks(), start=tmp.index(">ms2merged") + 1):
_mz, _int = tmp[idx].split(" ")
self.assertEqual(_peak, (float(_mz), float(_int)))
# Spectrum 2 -------------------
spec = MBSpectrum(os.path.join(os.path.dirname(__file__), "example_massbank_records", "EQ308406.txt"))
out = spec.to_sirius_format()
self.assertIn("EQ308406.ms", out)
self.assertIn("EQ308406.tsv", out)
self.assertIsNone(out["EQ308406.tsv"])
self.assertIn(">profile orbitrap", out["EQ308406.ms"])
# check fragmentation peaks
tmp = out["EQ308406.ms"].split("\n")
for idx, _peak in enumerate(spec.get_peaks(), start=tmp.index(">ms2merged") + 1):
_mz, _int = tmp[idx].split(" ")
self.assertEqual(_peak, (float(_mz), float(_int)))
# Spectrum 3 --------------------
spectra = []
acc = []
spec_cnt = 0
original_accessions = [
'EA000412', 'EA000414', 'EA000401', 'EA000413', 'EA000408', 'EA000409', 'EA000405', 'EA000402', 'EA000406',
'EA000404', 'EA000411', 'EA000403', 'EA000407', 'EA000410'
]
for oacc in original_accessions:
mb_fn = os.path.join(os.path.dirname(__file__), "example_massbank_records", "%s.txt" % oacc)
spectra.append(MBSpectrum(mb_fn))
acc.append(spectra[-1].get("accession"))
spec_cnt += 1
self.assertIn(
">ms2merged",
MBSpectrum.merge_spectra(spectra, merge_peak_lists=True).to_sirius_format()["EA33002987.ms"]
)
self.assertEqual(
spec_cnt,
MBSpectrum.merge_spectra(spectra, merge_peak_lists=False).to_sirius_format()["EA33002987.ms"].count(">ms2peaks")
)