def test_metainformation_merging__FIO00665(self):
# Apply merge function to a single spectrum
mb_fn = os.path.join(os.path.dirname(__file__), "example_massbank_records", "FIO00665.txt")
spec = MBSpectrum(mb_fn)
spectra = [spec]
acc_ref = [os.path.basename(mb_fn).split(".")[0]]
rt_ref = spec.get("retention_time")
precmz_ref = spec.get("precursor_mz")
recordtitle_ref = spec.get("record_title")
ce_ref = spec.get("collision_energy")
# -------------------
# WITH RT AGGREGATION
# -------------------
merged_spectrum = MBSpectrum.merge_spectra(spectra, rt_agg_fun=np.min) # type: MBSpectrum
self.assertEqual("FBZONXHGGPHHIY-UHFFFAOYSA-N", merged_spectrum.get("inchikey"))
self.assertEqual(acc_ref, merged_spectrum.get("original_accessions"))
self.assertEqual("FIO", merged_spectrum.get("accession")[:3])
self.assertEqual(MBSpectrum._get_new_accession_id(merged_spectrum.get("original_accessions")),
merged_spectrum.get("accession"))
self.assertEqual(rt_ref, merged_spectrum.get("retention_time"))
self.assertEqual(precmz_ref, merged_spectrum.get("precursor_mz"))
self.assertEqual(recordtitle_ref, merged_spectrum.get("record_title"))
self.assertEqual([ce_ref], merged_spectrum.get("collision_energy"))
def test_metainformation_merging__EAX000401(self):
# Load the list of spectra to merge: EA0004[01][0-9].txt --> EAX000401.txt
spectra = []
acc_ref = []
rt_ref = []
precmz_ref = []
recordtitle_ref = []
ce_ref = []
for mb_fn in glob.iglob(os.path.join(os.path.dirname(__file__), "example_massbank_records", "EA0004[01][0-9].txt")):
spectra.append(MBSpectrum(mb_fn))
# collect some reference meta-information
acc_ref.append(os.path.basename(mb_fn).split(".")[0])
rt_ref.append(spectra[-1].get("retention_time"))
precmz_ref.append(spectra[-1].get("precursor_mz"))
recordtitle_ref.append(spectra[-1].get("record_title"))
ce_ref.append(spectra[-1].get("collision_energy"))
# -------------------
# WITH RT AGGREGATION
# -------------------
merged_spectrum = MBSpectrum.merge_spectra(spectra, rt_agg_fun=np.mean) # type: MBSpectrum
self.assertEqual("OUSYWCQYMPDAEO-UHFFFAOYSA-N", merged_spectrum.get("inchikey"))
self.assertEqual(acc_ref, merged_spectrum.get("original_accessions"))
self.assertEqual("EA", merged_spectrum.get("accession")[:2])
self.assertEqual(MBSpectrum._get_new_accession_id(merged_spectrum.get("original_accessions")),
merged_spectrum.get("accession"))
self.assertEqual("min", merged_spectrum.get("retention_time_unit"))
self.assertEqual(np.mean(rt_ref), merged_spectrum.get("retention_time"))
self.assertEqual(precmz_ref[0], merged_spectrum.get("precursor_mz"))
self.assertEqual(recordtitle_ref, merged_spectrum.get("record_title"))
self.assertEqual(ce_ref, merged_spectrum.get("collision_energy"))
# ----------------------
# WITHOUT RT AGGREGATION
# ----------------------
merged_spectrum = MBSpectrum.merge_spectra(spectra, rt_agg_fun=None) # type: MBSpectrum
self.assertEqual("min", merged_spectrum.get("retention_time_unit"))
self.assertEqual(rt_ref, merged_spectrum.get("retention_time"))