From b68c07dee1182442d9da04dfc097721919e40ecd Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 19 Sep 2023 11:36:09 +0200 Subject: [PATCH 1/4] use proforma standard for tmt labeled modstrings --- spectrum_fundamentals/constants.py | 8 ++++---- spectrum_fundamentals/fragments.py | 5 +++-- tests/unit_tests/test_fragments.py | 9 +++++++-- tests/unit_tests/test_mod_string.py | 4 ++-- 4 files changed, 16 insertions(+), 10 deletions(-) diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py index 712e600..93c898f 100644 --- a/spectrum_fundamentals/constants.py +++ b/spectrum_fundamentals/constants.py @@ -73,16 +73,16 @@ "(ox)": "[UNIMOD:35]", "(Oxidation (M))": "[UNIMOD:35]", "(tm)": "[UNIMOD:737]", - "_(tm)": "_[UNIMOD:737]", + "_(tm)": "_[UNIMOD:737]-", "K(tm)": "K[UNIMOD:737]", "(i4)": "[UNIMOD:214]", - "_(i4)": "_[UNIMOD:214]", + "_(i4)": "_[UNIMOD:214]-", "K(i4)": "K[UNIMOD:214]", "(i8)": "[UNIMOD:730]", - "_(i8)": "_[UNIMOD:730]", + "_(i8)": "_[UNIMOD:730]-", "K(i8)": "K[UNIMOD:730]", "(tmp)": "[UNIMOD:2016]", - "_(tmp)": "_[UNIMOD:2016]", + "_(tmp)": "_[UNIMOD:2016]-", "K(tmp)": "K[UNIMOD:2016]", "(ph)": "[UNIMOD:21]", "(Phospho (STY))": "[UNIMOD:21]", diff --git a/spectrum_fundamentals/fragments.py b/spectrum_fundamentals/fragments.py index f8150d1..28f5c08 100644 --- a/spectrum_fundamentals/fragments.py +++ b/spectrum_fundamentals/fragments.py @@ -24,10 +24,11 @@ def _get_modifications(peptide_sequence: str) -> Optional[Tuple[Dict[int, float] modification_mass = constants.MOD_MASSES # Handle terminal modifications here for possible_tmt_mod in constants.TMT_MODS.values(): - if peptide_sequence.startswith(possible_tmt_mod): # TMT_6 + n_term_tmt = possible_tmt_mod + "-" + if peptide_sequence.startswith(n_term_tmt): tmt_n_term = 2 modification_deltas.update({0: constants.MOD_MASSES[possible_tmt_mod]}) - peptide_sequence = peptide_sequence[len(possible_tmt_mod) :] + peptide_sequence = peptide_sequence[len(n_term_tmt) :] break if "(" in peptide_sequence: diff --git a/tests/unit_tests/test_fragments.py b/tests/unit_tests/test_fragments.py index 9cb2993..b0cd7eb 100644 --- a/tests/unit_tests/test_fragments.py +++ b/tests/unit_tests/test_fragments.py @@ -18,11 +18,11 @@ def test_get_modifications_carbamidomethylation(self): def test_get_modifications_tmt_tag(self): """Test get_modifications.""" - assert fragments._get_modifications("[UNIMOD:737]ABC[UNIMOD:4]") == ({0: 229.162932, 2: 57.02146}, 2, "ABC") + assert fragments._get_modifications("[UNIMOD:737]-ABC[UNIMOD:4]") == ({0: 229.162932, 2: 57.02146}, 2, "ABC") def test_get_modifications_tmtpro_tag(self): """Test get_modifications.""" - assert fragments._get_modifications("[UNIMOD:2016]ABC[UNIMOD:4]") == ({0: 304.207146, 2: 57.02146}, 2, "ABC") + assert fragments._get_modifications("[UNIMOD:2016]-ABC[UNIMOD:4]") == ({0: 304.207146, 2: 57.02146}, 2, "ABC") class TestComputeMasses(unittest.TestCase): @@ -63,6 +63,11 @@ def test_compute_peptide_masses(self): seq = "SEQUENC[UNIMOD:4]E" self.assertEqual(fragments.compute_peptide_mass(seq), 1045.2561516699998) + def test_compute_peptide_masses_tmtpro(self): + """Test computation of peptide masses with valid input and tmt tag.""" + seq = "[UNIMOD:737]-SEQUENC[UNIMOD:4]E" + self.assertEqual(fragments.compute_peptide_mass(seq), 1274.41908367) + def test_compute_peptide_masses_with_invalid_syntax(self): """Negative testing of comuptation of peptide mass with unsupported syntax of mod string.""" seq = "SEQUEM(Ox.)CE" diff --git a/tests/unit_tests/test_mod_string.py b/tests/unit_tests/test_mod_string.py index 3f9fcc8..89dc7de 100644 --- a/tests/unit_tests/test_mod_string.py +++ b/tests/unit_tests/test_mod_string.py @@ -39,9 +39,9 @@ def test_maxquant_to_internal_variable_dehydration_long(self): def test_maxquant_to_internal_tmt(self): """Test maxquant_to_internal_tmt.""" - fixed_mods = {"C": "C[UNIMOD:4]", "^_": "_[UNIMOD:737]", "K": "K[UNIMOD:737]"} + fixed_mods = {"C": "C[UNIMOD:4]", "^_": "_[UNIMOD:737]-", "K": "K[UNIMOD:737]"} self.assertEqual( - mod.maxquant_to_internal(["_ABCDEFGHK_"], fixed_mods), ["[UNIMOD:737]ABC[UNIMOD:4]DEFGHK[UNIMOD:737]"] + mod.maxquant_to_internal(["_ABCDEFGHK_"], fixed_mods), ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHK[UNIMOD:737]"] ) def test_maxquant_to_internal_silac(self): From a88548c72e96d77b29008bb92026c577d77b63dd Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 19 Sep 2023 12:06:42 +0200 Subject: [PATCH 2/4] updated dependencies and limited python --- poetry.lock | 1196 +++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 584 insertions(+), 614 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5b7db0c..c0fee78 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -16,7 +15,6 @@ files = [ name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -35,7 +33,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.12.1" description = "Internationalization utilities" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -50,7 +47,6 @@ pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} name = "bandit" version = "1.7.5" description = "Security oriented static analyser for python code." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -72,33 +68,43 @@ yaml = ["PyYAML"] [[package]] name = "black" -version = "22.12.0" +version = "23.9.1" description = "The uncompromising code formatter." -category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - 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"pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [metadata] lock-version = "2.0" -python-versions = "^3.8.0" -content-hash = "87e638b36de0b820e63a88b39366e299f870a668354fef0a5e9ca778da003613" +python-versions = ">=3.8.0,<3.11.0" +content-hash = "896128af4c53517eae6bbbcf64a3af4985139401e37a3212cb6d602e0d323526" diff --git a/pyproject.toml b/pyproject.toml index 127c437..3b502b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ classifiers = [ [tool.poetry.dependencies] -python = "^3.8.0" +python = ">=3.8.0,<3.11.0" click = ">=8.0.0" rich = ">=10.3.0" PyYAML = ">=5.4.1" From 9a84eee238f6a28e48323d965370d2cef048c76d Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 19 Sep 2023 17:13:01 +0200 Subject: [PATCH 3/4] fix mass tol and unit not forwarded --- spectrum_fundamentals/fragments.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spectrum_fundamentals/fragments.py b/spectrum_fundamentals/fragments.py index 28f5c08..55fe022 100644 --- a/spectrum_fundamentals/fragments.py +++ b/spectrum_fundamentals/fragments.py @@ -184,7 +184,7 @@ def initialize_peaks( for ion_type in range(0, number_of_ion_types): # generate all ion types # Check for neutral loss here mass = (ion_type_masses[ion_type] + charge_delta) / charge - min_mass, max_mass = get_min_max_mass(mass_analyzer, mass) + min_mass, max_mass = get_min_max_mass(mass_analyzer, mass, mass_tolerance, unit_mass_tolerance) fragments_meta_data.append( { "ion_type": ion_types[ion_type], # ion type From bcc135574cd08722416f51f9e121249cc817925c Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 19 Sep 2023 17:35:18 +0200 Subject: [PATCH 4/4] remove duplicate key --- spectrum_fundamentals/constants.py | 1 - 1 file changed, 1 deletion(-) diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py index 93c898f..e23207f 100644 --- a/spectrum_fundamentals/constants.py +++ b/spectrum_fundamentals/constants.py @@ -49,7 +49,6 @@ "C[UNIMOD:4]": 2, "K[UNIMOD:737]": 22, "K[UNIMOD:2016]": 22, - "K[UNIMOD:2016]": 22, "K[UNIMOD:214]": 22, "K[UNIMOD:730]": 22, "S[UNIMOD:21]": 25,