diff --git a/spectrum_fundamentals/fragments.py b/spectrum_fundamentals/fragments.py index 3c2233e..b8e6497 100644 --- a/spectrum_fundamentals/fragments.py +++ b/spectrum_fundamentals/fragments.py @@ -181,7 +181,7 @@ def initialize_peaks( if modification_deltas: # there were modifictions sequence = internal_without_mods([sequence])[0] - n_term_delta = modification_deltas.get(-2, 0.0) + n_term_delta = modification_deltas.pop(-2, 0.0) # directly pop it to avoid readding it later if n_term_delta != 0: n_term_mod = 2 # add n_term mass to first aa for easy processing in the following calculation diff --git a/tests/unit_tests/data/tmt_spectrum_input.json b/tests/unit_tests/data/tmt_spectrum_input.json new file mode 100644 index 0000000..5ce0851 --- /dev/null +++ b/tests/unit_tests/data/tmt_spectrum_input.json @@ -0,0 +1,1875 @@ +{ + "MODIFIED_SEQUENCE": { + "0": "[UNIMOD:737]-AAAAAAAAAVSRR", + "1": "[UNIMOD:737]-AAAAALRR", + "2": "[UNIMOD:737]-AAAAPNK[UNIMOD:737]", + "3": 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test_annotate_spectra_tmt(self): + """Test annotate spectra.""" + spectrum_input = pd.read_json( + Path(__file__).parent / "data/tmt_spectrum_input.json", + # converters={"INTENSITIES": literal_eval, "MZ": literal_eval}, + ) + expected_result = pd.read_json( + Path(__file__).parent / "data/tmt_spectrum_output.json", + ) + + result = annotation.annotate_spectra(spectrum_input) + pd.testing.assert_frame_equal(expected_result, result) + def test_handle_multiple_matches(self): """Test handle_multiple_matches function.""" # Example input data with multiple matches. They don't make biological sense but it tests the mathematical correctness.