From 690f490e47d45db4259c17ee938eef9f55145f96 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 12 Aug 2024 15:38:25 +0200 Subject: [PATCH] fixed mz calc with n_term mod --- spectrum_fundamentals/fragments.py | 2 +- tests/unit_tests/data/tmt_spectrum_input.json | 1875 +++++++++++++++++ .../unit_tests/data/tmt_spectrum_output.json | 241 +++ tests/unit_tests/test_annotation.py | 13 + 4 files changed, 2130 insertions(+), 1 deletion(-) create mode 100644 tests/unit_tests/data/tmt_spectrum_input.json create mode 100644 tests/unit_tests/data/tmt_spectrum_output.json 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": "[UNIMOD:737]-AAAARC[UNIMOD:4]GQHGEPFK[UNIMOD:737]", + "4": "[UNIMOD:737]-AAADFATHGK[UNIMOD:737]" + }, + "PEPTIDE_LENGTH": { "0": 13, "1": 8, "2": 7, "3": 14, "4": 10 }, + "MASS_ANALYZER": { + "0": "ITMS", + "1": "ITMS", + "2": "ITMS", + "3": "ITMS", + "4": "ITMS" + }, + "PRECURSOR_CHARGE": { "0": 2, "1": 3, "2": 2, "3": 3, "4": 3 }, + "INTENSITIES": { + "0": [ + 5.2444424629, 6.1402797699, 8.571393013, 18.1187095642, + 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"CALCULATED_MASS": { + "0": 1384.81018667, + "1": 1027.64535267, + "2": 1099.67553867, + "3": 1957.03579667, + "4": 1445.80325967 + }, + "removed_peaks": { "0": 0, "1": 0, "2": 1, "3": 0, "4": 0 } +} diff --git a/tests/unit_tests/test_annotation.py b/tests/unit_tests/test_annotation.py index f888031..cb73174 100644 --- a/tests/unit_tests/test_annotation.py +++ b/tests/unit_tests/test_annotation.py @@ -73,6 +73,19 @@ def test_annotate_spectra_cl_xl(self): result = annotation.annotate_spectra(spectrum_input) pd.testing.assert_frame_equal(expected_result, result) + def 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.