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Fix empty class annotation bug #252

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merged 2 commits into from
Aug 9, 2024
Merged

Fix empty class annotation bug #252

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ffe805d
Added test, to detect bug.
niekdejonge Aug 7, 2024
64824e7
Fixed bug
niekdejonge Aug 7, 2024
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2 changes: 1 addition & 1 deletion ms2query/create_new_library/add_classifire_classifications.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,7 @@ def select_compound_classes(spectra):
break
if cf_classes is None:
print(f"no classyfire annotation was found for inchikey {inchikey14}")
inchikey_results_list[i].append([inchikey14, "", "", "", "", ""])
inchikey_results_list[i] += ["", "", "", "", ""]

# select NPC classes
npc_results = None
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7 changes: 7 additions & 0 deletions tests/test_add_classifier_annotations.py
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Expand Up @@ -23,3 +23,10 @@ def test_add_classifier_annotation(spectra):
result = select_compound_classes(spectra)
assert sorted(result) == [['WRIPSIKIDAUKBP', 'Organic compounds', 'Phenylpropanoids and polyketides', 'Macrolactams', '', 'Macrolactams', '', '', 'Alkaloids', 'False'],
['WXDBUBIFYCCNLE', 'Organic compounds', 'Organoheterocyclic compounds', 'Oxepanes', '', 'Oxepanes', 'Lipopeptides', 'Oligopeptides', 'Amino acids and Peptides', 'False']]


def test_add_classifier_annotation_unknown_inchikey(spectra):
"""This tests that when no compound class annotation is found, that it is correctly filled with empty strings"""
spectra[1].set("inchikey", "AAAAAAAAAAAAAA")
result = select_compound_classes(spectra)
assert len(result[0]) == len(result[1])
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