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"18b42a9d036dfcb0032e83aa43799a266362b2cfe35a1008c99a2ca9fd2d8468" diff --git a/pyproject.toml b/pyproject.toml index 6081667..3cdae18 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,15 +12,13 @@ packages = [ { include = "spectrum_fundamentals" }, ] classifiers = [ - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", ] [tool.poetry.dependencies] -python = ">=3.8.0,<3.11.0" +python = ">=3.9.0,<3.11.0" click = ">=8.0.0" rich = ">=10.3.0" PyYAML = ">=5.4.1" diff --git a/spectrum_fundamentals/annotation/annotation.py b/spectrum_fundamentals/annotation/annotation.py index 98dbd81..5eec9f2 100644 --- a/spectrum_fundamentals/annotation/annotation.py +++ b/spectrum_fundamentals/annotation/annotation.py @@ -5,7 +5,7 @@ import pandas as pd from spectrum_fundamentals import constants -from spectrum_fundamentals.fragments import initialize_peaks, initialize_peaks_xl +from spectrum_fundamentals.fragments import initialize_peaks, initialize_peaks_xl, retrieve_ion_types logger = logging.getLogger(__name__) @@ -31,11 +31,10 @@ def match_peaks( """ start_peak = 0 no_of_peaks = len(peaks_intensity) - max_intensity = 1.0 + max_intensity = 0.0 row_list = [] temp_list = [] next_start_peak = 0 - seq_len = len(unmod_sequence) matched_peak = False fragment_no: float for fragment in fragments_meta_data: @@ -55,7 +54,7 @@ def match_peaks( start_peak += 1 continue if ( - not (fragment["ion_type"] == "b" and fragment_no == 1) + not (fragment["ion_type"][0] == "b" and fragment_no == 1) or (unmod_sequence[0] == "R" or unmod_sequence[0] == "H" or unmod_sequence[0] == "K") and (tmt_n_term == 1) ): @@ -69,7 +68,7 @@ def match_peaks( "intensity": peak_intensity, } ) - if peak_intensity > max_intensity and fragment_no < seq_len: + if peak_intensity > max_intensity: max_intensity = float(peak_intensity) matched_peak = True next_start_peak = start_peak @@ -119,7 +118,10 @@ def handle_multiple_matches( def annotate_spectra( - un_annot_spectra: pd.DataFrame, mass_tolerance: Optional[float] = None, unit_mass_tolerance: Optional[str] = None + un_annot_spectra: pd.DataFrame, + mass_tolerance: Optional[float] = None, + unit_mass_tolerance: Optional[str] = None, + fragmentation_method: str = "HCD", ) -> pd.DataFrame: """ Annotate a set of spectra. @@ -138,12 +140,13 @@ def annotate_spectra( :param un_annot_spectra: a Pandas DataFrame containing the raw peaks and metadata to be annotated :param mass_tolerance: mass tolerance to calculate min and max mass :param unit_mass_tolerance: unit for the mass tolerance (da or ppm) + :param fragmentation_method: fragmentation method that was used :return: a Pandas DataFrame containing the annotated spectra with meta data """ raw_file_annotations = [] index_columns = {col: un_annot_spectra.columns.get_loc(col) for col in un_annot_spectra.columns} for row in un_annot_spectra.values: - results = parallel_annotate(row, index_columns, mass_tolerance, unit_mass_tolerance) + results = parallel_annotate(row, index_columns, mass_tolerance, unit_mass_tolerance, fragmentation_method) if not results: continue raw_file_annotations.append(results) @@ -269,7 +272,7 @@ def generate_annotation_matrix_xl( def generate_annotation_matrix( - matched_peaks: pd.DataFrame, unmod_seq: str, charge: int + matched_peaks: pd.DataFrame, unmod_seq: str, charge: int, fragmentation_method: str = "HCD" ) -> Tuple[np.ndarray, np.ndarray]: """ Generate the annotation matrix in the prosit format from matched peaks. @@ -277,16 +280,21 @@ def generate_annotation_matrix( :param matched_peaks: matched peaks needed to be converted :param unmod_seq: Un modified peptide sequence :param charge: Precursor charge + :param fragmentation_method: fragmentation method that was used :return: numpy array of intensities and numpy array of masses """ - intensity = np.full(constants.VEC_LENGTH, -1.0) - mass = np.full(constants.VEC_LENGTH, -1.0) + ion_types = retrieve_ion_types(fragmentation_method) + charge_const = 3 + vec_length = (constants.SEQ_LEN - 1) * charge_const * len(ion_types) + + intensity = np.full(vec_length, -1.0) + mass = np.full(vec_length, -1.0) # change values to zeros if len(unmod_seq) < constants.SEQ_LEN: - peaks_range = range(0, ((len(unmod_seq) - 1) * 6)) + peaks_range = range(0, ((len(unmod_seq) - 1) * charge_const * len(ion_types))) else: - peaks_range = range(0, ((constants.SEQ_LEN - 1) * 6)) + peaks_range = range(0, ((constants.SEQ_LEN - 1) * charge_const * len(ion_types))) if charge == 1: available_peaks = [index for index in peaks_range if (index % 3 == 0)] @@ -305,10 +313,8 @@ def generate_annotation_matrix( exp_mass_col = matched_peaks.columns.get_loc("exp_mass") for peak in matched_peaks.values: - if peak[ion_type].startswith("y"): - peak_pos = ((peak[no_col] - 1) * 6) + (peak[charge_col] - 1) - else: - peak_pos = ((peak[no_col] - 1) * 6) + (peak[charge_col] - 1) + 3 + ion_type_index = ion_types.index(peak[ion_type][0]) + peak_pos = ((peak[no_col] - 1) * charge_const * len(ion_types)) + (peak[charge_col] - 1) + 3 * ion_type_index if peak_pos >= constants.VEC_LENGTH: continue @@ -316,7 +322,9 @@ def generate_annotation_matrix( mass[peak_pos] = peak[exp_mass_col] if len(unmod_seq) < constants.SEQ_LEN: - mask_peaks = range((len(unmod_seq) - 1) * 6, ((len(unmod_seq) - 1) * 6) + 6) + mask_peaks = range( + (len(unmod_seq) - 1) * charge_const * len(ion_types), ((len(unmod_seq)) * charge_const * len(ion_types)) + ) intensity[mask_peaks] = -1.0 mass[mask_peaks] = -1.0 @@ -328,6 +336,7 @@ def parallel_annotate( index_columns: Dict[str, int], mass_tolerance: Optional[float] = None, unit_mass_tolerance: Optional[str] = None, + fragmentation_method: str = "HCD", ) -> Optional[ Union[ Tuple[np.ndarray, np.ndarray, float, int], @@ -348,6 +357,7 @@ def parallel_annotate( :param index_columns: a dictionary that contains the index columns of the spectrum :param mass_tolerance: mass tolerance to calculate min and max mass :param unit_mass_tolerance: unit for the mass tolerance (da or ppm) + :param fragmentation_method: fragmentation method that was used :return: a tuple containing intensity values (np.ndarray), masses (np.ndarray), calculated mass (float), and any removed peaks (List[str]) """ @@ -355,7 +365,9 @@ def parallel_annotate( if xl_type_col is None: if spectrum[index_columns["PEPTIDE_LENGTH"]] > 30: # this was in initialize peaks but can be checked prior return None - return _annotate_linear_spectrum(spectrum, index_columns, mass_tolerance, unit_mass_tolerance) + return _annotate_linear_spectrum( + spectrum, index_columns, mass_tolerance, unit_mass_tolerance, fragmentation_method + ) if (spectrum[index_columns["PEPTIDE_LENGTH_A"]] > 30) or (spectrum[index_columns["PEPTIDE_LENGTH_B"]] > 30): return None @@ -369,6 +381,7 @@ def _annotate_linear_spectrum( index_columns: Dict[str, int], mass_tolerance: Optional[float], unit_mass_tolerance: Optional[str], + fragmentation_method: str = "HCD", ): """ Annotate a linear peptide spectrum. @@ -377,17 +390,19 @@ def _annotate_linear_spectrum( :param index_columns: Index columns of the spectrum :param mass_tolerance: Mass tolerance for calculating min and max mass :param unit_mass_tolerance: Unit for the mass tolerance (da or ppm) + :param fragmentation_method: fragmentation method that was used :return: Annotated spectrum """ mod_seq_column = "MODIFIED_SEQUENCE" if "MODIFIED_SEQUENCE_MSA" in index_columns: mod_seq_column = "MODIFIED_SEQUENCE_MSA" fragments_meta_data, tmt_n_term, unmod_sequence, calc_mass = initialize_peaks( - spectrum[index_columns[mod_seq_column]], - spectrum[index_columns["MASS_ANALYZER"]], - spectrum[index_columns["PRECURSOR_CHARGE"]], - mass_tolerance, - unit_mass_tolerance, + sequence=spectrum[index_columns[mod_seq_column]], + mass_analyzer=spectrum[index_columns["MASS_ANALYZER"]], + charge=spectrum[index_columns["PRECURSOR_CHARGE"]], + mass_tolerance=mass_tolerance, + unit_mass_tolerance=unit_mass_tolerance, + fragmentation_method=fragmentation_method, ) matched_peaks = match_peaks( fragments_meta_data, @@ -398,14 +413,18 @@ def _annotate_linear_spectrum( spectrum[index_columns["PRECURSOR_CHARGE"]], ) + ion_types = retrieve_ion_types(fragmentation_method) + charge_const = 3 + vec_length = (constants.SEQ_LEN - 1) * charge_const * len(ion_types) + if len(matched_peaks) == 0: - intensity = np.full(174, 0.0) - mass = np.full(174, 0.0) + intensity = np.full(vec_length, 0.0) + mass = np.full(vec_length, 0.0) return intensity, mass, calc_mass, 0 matched_peaks, removed_peaks = handle_multiple_matches(matched_peaks) intensities, mass = generate_annotation_matrix( - matched_peaks, unmod_sequence, spectrum[index_columns["PRECURSOR_CHARGE"]] + matched_peaks, unmod_sequence, spectrum[index_columns["PRECURSOR_CHARGE"]], fragmentation_method ) return intensities, mass, calc_mass, removed_peaks diff --git a/spectrum_fundamentals/fragments.py b/spectrum_fundamentals/fragments.py index b781e75..5f058d2 100644 --- a/spectrum_fundamentals/fragments.py +++ b/spectrum_fundamentals/fragments.py @@ -81,6 +81,50 @@ def _xl_sanity_check(noncl_xl: int, peptide_beta_mass: float, xl_pos: float): raise ValueError("Crosslinker position must be provided if using non cleavable XL mode.") +def retrieve_ion_types(fragmentation_method: str) -> List[str]: + """ + Retrieve the ion types resulting from a fragmentation method. + + Given the fragmentation method the function returns all ion types that can result from it. + + : param fragmentation_method: fragmentation method used during the MS + : raises ValueError: if fragmentation_method is other than one of HCD, CID, ETD, ECD, ETCID, ETHCD, UVPD + : return: list of possible ion types + """ + fragmentation_method = fragmentation_method.upper() + if fragmentation_method == "HCD" or fragmentation_method == "CID": + return ["y", "b"] + elif fragmentation_method == "ETD" or fragmentation_method == "ECD": + return ["z", "c"] + elif fragmentation_method == "ETCID" or fragmentation_method == "ETHCD": + return ["y", "z", "b", "c"] + elif fragmentation_method == "UVPD": + return ["x", "y", "z", "a", "b", "c"] + else: + raise ValueError(f"Unknown fragmentation method provided: {fragmentation_method}") + + +def get_ion_delta(ion_types: List[str]) -> np.ndarray: + """ + Calculate the mass of an ion. + + :param ion_types: type of ions for which mass should be calculated + :return: numpy array with masses of the ions + """ + ion_type_offsets = { + "a": -constants.ATOM_MASSES["O"] - constants.ATOM_MASSES["C"], + "b": 0.0, + "c": 3 * constants.ATOM_MASSES["H"] + constants.ATOM_MASSES["N"], + "x": 2 * constants.ATOM_MASSES["O"] + constants.ATOM_MASSES["C"], + "y": constants.ATOM_MASSES["O"] + 2 * constants.ATOM_MASSES["H"], + "z": constants.ATOM_MASSES["O"] - constants.ATOM_MASSES["N"] - constants.ATOM_MASSES["H"], + } + # I think list comprehension is fastest way + deltas = np.array([ion_type_offsets[ion_type] for ion_type in ion_types]).reshape(len(ion_types), 1) + + return deltas + + def initialize_peaks( sequence: str, mass_analyzer: str, @@ -90,6 +134,7 @@ def initialize_peaks( noncl_xl: bool = False, peptide_beta_mass: float = 0.0, xl_pos: int = -1, + fragmentation_method: str = "HCD", ) -> Tuple[List[dict], int, str, float]: """ Generate theoretical peaks for a modified peptide sequence. @@ -102,24 +147,25 @@ def initialize_peaks( :param noncl_xl: whether the function is called with a non-cleavable xl modification :param peptide_beta_mass: the mass of the second peptide to be considered for non-cleavable XL :param xl_pos: the position of the crosslinker for non-cleavable XL + :param fragmentation_method: fragmentation method that was used :return: List of theoretical peaks, Flag to indicate if there is a tmt on n-terminus, Un modified peptide sequence """ _xl_sanity_check(noncl_xl, peptide_beta_mass, xl_pos) max_charge = min(3, charge) - ion_type_offsets = [0.0, constants.ATOM_MASSES["O"] + 2 * constants.ATOM_MASSES["H"]] - - # tmp place holder - ion_type_masses = [0.0, 0.0] - ion_types = ["b", "y"] + ion_types = retrieve_ion_types(fragmentation_method) + modification_deltas = _get_modifications(sequence) - number_of_ion_types = len(ion_type_offsets) fragments_meta_data = [] - - modification_deltas = _get_modifications(sequence) - forward_sum = 0.0 # sum over all amino acids from left to right (neutral charge) - backward_sum = 0.0 # sum over all amino acids from right to left (neutral charge) n_term_mod = 1 + + if noncl_xl: + # the test only needs to be done because the unit tests use non_cl_xl peptides + # without a crosslinker modification. This cannot occur in nature!!! + # The unit tests need to be changed, then we can simply add to the existing + # modification mass at xl_pos -1. + modification_deltas[xl_pos - 1] = modification_deltas.get(xl_pos - 1, 0.0) + peptide_beta_mass + if modification_deltas: # there were modifictions sequence = internal_without_mods([sequence])[0] n_term_delta = modification_deltas.get(-2, 0.0) @@ -128,62 +174,52 @@ def initialize_peaks( # add n_term mass to first aa for easy processing in the following calculation modification_deltas[0] = modification_deltas.get(0, 0.0) + n_term_delta - # calculation: - - peptide_length = len(sequence) - for i in range(peptide_length): # generate substrings - forward_sum += constants.AA_MASSES[sequence[i]] # sum left to right - if i in modification_deltas: # add mass of modification if present - forward_sum += modification_deltas[i] - backward_sum += constants.AA_MASSES[sequence[peptide_length - i - 1]] # sum right to left - if peptide_length - i - 1 in modification_deltas: # add mass of modification if present - backward_sum += modification_deltas[peptide_length - i - 1] - - ion_type_masses[0] = forward_sum + ion_type_offsets[0] # b ion - ... - - ion_type_masses[1] = backward_sum + ion_type_offsets[1] # y ion - - for charge in range(constants.MIN_CHARGE, max_charge + 1): # generate ion in different charge states - # positive charge is introduced by protons (or H - ELECTRON_MASS) - charge_delta = charge * constants.PARTICLE_MASSES["PROTON"] - for ion_type in range(number_of_ion_types): # generate all ion types - mass = _compute_ion_mass( - ion_mass=ion_type_masses[ion_type], - noncl_xl=noncl_xl, - ion_type=ion_type, - xl_pos=xl_pos, - peptide_beta_mass=peptide_beta_mass, - peptide_length=peptide_length, - i=i, - ) - mz = (mass + charge_delta) / charge - min_mz, max_mz = get_min_max_mass(mass_analyzer, mz, mass_tolerance, unit_mass_tolerance) - + mass_arr = np.array([constants.AA_MASSES[_] for _ in sequence]) + for pos, mod_mass in modification_deltas.items(): + mass_arr[pos] += mod_mass + + n_forward_ions = len(ion_types) // 2 + n_fragments = len(sequence) - 1 + sum_array = np.empty(shape=(len(ion_types), n_fragments)) + np.cumsum(mass_arr[:0:-1], out=sum_array[0]) # this is for the reverse ion-series + np.cumsum(mass_arr[:-1], out=sum_array[n_forward_ions]) # this is for the forward ion-series + peptide_mass = sum_array[0, -1] + mass_arr[0] # this is the longest reverse ion + the first residue + + # get offset for all needed ions + deltas = get_ion_delta(ion_types) + np.add(sum_array[0], deltas[:n_forward_ions], out=sum_array[:n_forward_ions]) + np.add(sum_array[n_forward_ions], deltas[n_forward_ions:], out=sum_array[n_forward_ions:]) + + # calculate for m/z for charges 1, 2, 3 + # shape of ion_mzs: (n_ions, n_fragments, max_charge) + charges = np.arange(1, max_charge + 1) + ion_mzs = (sum_array[..., np.newaxis] + charges * constants.PARTICLE_MASSES["PROTON"]) / charges + + min_mzs, max_mzs = get_min_max_mass(mass_analyzer, ion_mzs, mass_tolerance, unit_mass_tolerance) + + # write mz together with min and max value in output list with one dictionary for each ion + for ion_type in range(len(ion_types)): + for number in range(n_fragments): + for charge in range(max_charge): fragments_meta_data.append( { "ion_type": ion_types[ion_type], # ion type - "no": i + 1, # no - "charge": charge, # charge - "mass": mz, # mz - "min_mass": min_mz, # min mz - "max_mass": max_mz, # max mz + "no": number + 1, # no + "charge": charge + 1, # charge + "mass": ion_mzs[ion_type, number, charge], # mz + "min_mass": min_mzs[ion_type, number, charge], # min mz + "max_mass": max_mzs[ion_type, number, charge], # max mz } ) - fragments_meta_data = sorted(fragments_meta_data, key=itemgetter("mass")) - return fragments_meta_data, n_term_mod, sequence, (forward_sum + ion_type_offsets[0] + ion_type_offsets[1]) + fragments_meta_data = sorted(fragments_meta_data, key=itemgetter("mass")) -def _compute_ion_mass( - ion_mass: float, noncl_xl: bool, ion_type: int, xl_pos: int, peptide_beta_mass: float, peptide_length: int, i: int -) -> float: - # Check for neutral loss here - - if noncl_xl and ((ion_type == 0 and i + 1 >= xl_pos) or (ion_type == 1 and i >= peptide_length - xl_pos)): - mass = ion_mass + peptide_beta_mass - else: - mass = ion_mass - - return mass + return ( + fragments_meta_data, + n_term_mod, + sequence, + (peptide_mass + constants.ATOM_MASSES["O"] + 2 * constants.ATOM_MASSES["H"]), + ) def initialize_peaks_xl( @@ -309,8 +345,11 @@ def initialize_peaks_xl( def get_min_max_mass( - mass_analyzer: str, mass: float, mass_tolerance: Optional[float] = None, unit_mass_tolerance: Optional[str] = None -) -> Tuple[float, float]: + mass_analyzer: str, + mass: np.ndarray, + mass_tolerance: Optional[float] = None, + unit_mass_tolerance: Optional[str] = None, +) -> Tuple[np.ndarray, np.ndarray]: """Helper function to get min and max mass based on mass analyzer. If both mass_tolerance and unit_mass_tolerance are provided, the function uses the provided tolerance diff --git a/spectrum_fundamentals/metrics/similarity.py b/spectrum_fundamentals/metrics/similarity.py index 930df61..24f81c5 100644 --- a/spectrum_fundamentals/metrics/similarity.py +++ b/spectrum_fundamentals/metrics/similarity.py @@ -171,9 +171,9 @@ def spectral_entropy_similarity( :param predicted_intensities: predicted intensities, see observed_intensities for details, array of length 174 :return: spectral entropy similarity values """ - if type(observed_intensities) == scipy.sparse.csr_matrix: + if isinstance(observed_intensities, scipy.sparse.csr_matrix): observed_intensities = observed_intensities.toarray() - if type(predicted_intensities) == scipy.sparse.csr_matrix: + if isinstance(predicted_intensities, scipy.sparse.csr_matrix): predicted_intensities = predicted_intensities.toarray() entropies = [] diff --git a/tests/unit_tests/data/annotation_xl_cl_output.json b/tests/unit_tests/data/annotation_xl_cl_output.json index 049d8e1..5cc3a99 100644 --- a/tests/unit_tests/data/annotation_xl_cl_output.json +++ b/tests/unit_tests/data/annotation_xl_cl_output.json @@ -1,6 +1,6 @@ -[ - { - "INTENSITIES_A": [ +{ + "INTENSITIES_A": { + "0": [ 1.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, @@ -33,11 +33,14 @@ -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0 ], - "INTENSITIES_B": [ - 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, - 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, - -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 1.0, 0.0, - -1.0, 0.0, 0.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, + "1": [ + 0.5336033987, 0.0, -1.0, 0.0, 0.0, -1.0, 0.4464429494, 0.0, -1.0, + 0.2501760443, 0.0, -1.0, 0.6483555549, 0.051478993, -1.0, + 0.0193635044, 0.0, -1.0, 0.1885797428, 0.1646983684, -1.0, + 0.0301492272, 0.0, -1.0, 0.04490012, 0.0580133805, -1.0, 0.0, 0.0, + -1.0, 0.0942211574, 0.8777324399, -1.0, 0.0085736376, 0.0, -1.0, + 0.0149206348, 1.0, -1.0, 0.0087054536, 0.0, -1.0, -1.0, -1.0, -1.0, + -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, @@ -49,10 +52,11 @@ -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, - -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, 0.0, 0.0, -1.0, -1.0, - -1.0, -1.0, 0.0, 0.0, -1.0, -1.0, -1.0, -1.0, 0.0, 0.0, -1.0, -1.0, - -1.0, -1.0, 0.0, 0.0, -1.0, -1.0, -1.0, -1.0, 0.0, 0.0, -1.0, -1.0, - -1.0, -1.0, 0.0, 0.0, -1.0, -1.0, -1.0, -1.0, 0.0, 0.0, -1.0, -1.0, + -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, + -1.0, -1.0, -1.0, -1.0, 0.2228325182, 0.0804106443, -1.0, -1.0, + -1.0, -1.0, 0.0766443917, 0.0390705762, -1.0, 0.0, 0.0, -1.0, + 0.3271260935, 0.3874682711, -1.0, 0.0300429577, 0.0, -1.0, + 0.0935432716, 0.4449355698, -1.0, 0.0381732187, 0.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, @@ -66,12 +70,14 @@ -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0 ], - "MZ_A": [ - 175.1189422607, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, - -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, - -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, - -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, - -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, + "2": [ + 0.2702024343, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0621895043, 0.0, -1.0, + 0.0, 0.0, -1.0, 0.0797492196, 0.0086173282, -1.0, 0.0, 0.0, -1.0, + 1.0, 0.0478354978, -1.0, 0.0112539558, 0.0, -1.0, 0.0, 0.0, -1.0, + 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, + 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, + -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, + -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, @@ -83,11 +89,10 @@ -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, - 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-1.0, -1.0, -1.0, -1.0 + -1.0, -1.0, -1.0, -1.0, -1.0, -1.0 ], - "MZ_B": [ - 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, - 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, - -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, - 838.4536132812, 0.0, -1.0, 0.0, 0.0, -1.0, -1.0, -1.0, -1.0, -1.0, + "3": [ + 1.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0375893094, 0.0, + -1.0, 0.029594885, 0.0, -1.0, 0.058867643, 0.0, -1.0, 0.0, 0.0, + -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0264563199, 0.0, -1.0, 0.0, + 0.0, -1.0, 0.0651580902, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, + 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, @@ -115,11 +121,10 @@ -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, 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"min_mass": 557.2341901252994, + "max_mass": 557.2564799387007 + }, + { + "ion_type": "y", + "no": 5, + "charge": 1, + "mass": 574.271884137, + "min_mass": 574.2603986993173, + "max_mass": 574.2833695746828 + }, + { + "ion_type": "x", + "no": 5, + "charge": 1, + "mass": 600.251148667, + "min_mass": 600.2391436440267, + "max_mass": 600.2631536899734 + }, + { + "ion_type": "a", + "no": 6, + "charge": 1, + "mass": 625.3191688669999, + "min_mass": 625.3066624836226, + "max_mass": 625.3316752503772 + }, + { + "ion_type": "b", + "no": 6, + "charge": 1, + "mass": 653.3140834669999, + "min_mass": 653.3010171853306, + "max_mass": 653.3271497486693 + }, + { + "ion_type": "c", + "no": 6, + "charge": 1, + "mass": 670.3406325719999, + "min_mass": 670.3272257593485, + "max_mass": 670.3540393846513 + }, + { + "ion_type": "z", + "no": 6, + "charge": 1, + "mass": 686.2879280320001, + "min_mass": 686.2742022734394, + "max_mass": 686.3016537905607 + }, + { + "ion_type": "y", + "no": 6, + "charge": 1, + "mass": 703.314477137, + "min_mass": 703.3004108474573, + "max_mass": 703.3285434265428 + }, + { + "ion_type": "x", + "no": 6, + "charge": 1, + "mass": 729.2937416670001, + "min_mass": 729.2791557921668, + "max_mass": 729.3083275418334 + } +] diff --git a/tests/unit_tests/test_fragments.py b/tests/unit_tests/test_fragments.py index b45e5b2..40448c2 100644 --- a/tests/unit_tests/test_fragments.py +++ b/tests/unit_tests/test_fragments.py @@ -7,123 +7,23 @@ import spectrum_fundamentals.fragments as fragments -class TestGetModifications: - """Class to test get modifications.""" - - def test_get_modifications(self): - """Test get_modifications.""" - assert fragments._get_modifications("ABC") == {} - - def test_get_modifications_carbamidomethylation(self): - """Test get_modifications.""" - assert fragments._get_modifications("ABC[UNIMOD:4]") == {2: 57.021464} - - def test_get_modifications_tmt_tag(self): - """Test get_modifications.""" - assert fragments._get_modifications("[UNIMOD:737]-ABC[UNIMOD:4]") == {-2: 229.162932, 2: 57.021464} - - def test_get_modifications_tmtpro_tag(self): - """Test get_modifications.""" - assert fragments._get_modifications("[UNIMOD:2016]-ABC[UNIMOD:4]") == {-2: 304.207146, 2: 57.021464} - - -class TestComputeMasses(unittest.TestCase): - """Class to test compute ion and peptide masses.""" - - def test_compute_ion_masses(self): - """ - Test compute ion masses. - - >>> from pyteomics import mass - >>> mass.calculate_mass(sequence='AD', ion_type='b', charge=1) - """ - masses = fragments.compute_ion_masses([1, 3, 4] + [0] * 27, [1, 0, 0, 0, 0, 0]) # peptide = ADE, charge = 1 - assert_almost_equal(masses[0], 148.06044, decimal=5) # y1 E.- - assert_almost_equal(masses[1], -1.0, decimal=5) # y1;2+: n.a. - assert_almost_equal(masses[3], 72.04439, decimal=5) # b1: -.A - assert_almost_equal(masses[6], 263.08738, decimal=5) # y2 DE.- - assert_almost_equal(masses[9], 187.07133, decimal=5) # b2: -.AD - - def test_compute_ion_masses_tmtpro(self): - """ - Test compute ion masses. - - >>> from pyteomics import mass - >>> mass.calculate_mass(sequence='AD', ion_type='b', charge=1) - """ - masses = fragments.compute_ion_masses( - [1, 3, 4] + [0] * 27, [1, 0, 0, 0, 0, 0], "tmtpro" - ) # peptide = [UNIMOD:2016]ADE, charge = 1 - assert_almost_equal(masses[0], 148.06044, decimal=5) # y1 E.- - assert_almost_equal(masses[1], -1.0, decimal=5) # y1;2+: n.a. - assert_almost_equal(masses[3], 72.04439 + 304.207146, decimal=5) # b1: -.A - assert_almost_equal(masses[6], 263.08738, decimal=5) # y2 DE.- - self.assertAlmostEqual(masses[9], 187.07133 + 304.207146, places=5) # b2: -.AD - - def test_compute_peptide_masses(self): - """Test computation of peptide masses with valid input.""" - seq = "SEQUENC[UNIMOD:4]E" - self.assertEqual(fragments.compute_peptide_mass(seq), 1045.2561556699998) - - 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), 1274.41908767) - - 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" - self.assertRaises(KeyError, fragments.compute_peptide_mass, seq) - - def test_compute_peptide_masses_with_invalid_mod(self): - """Negative testing of computation of peptide mass with unknown modification in mod string.""" - seq = "SEQUENC[UNIMOD:0]E" - self.assertRaises(KeyError, fragments.compute_peptide_mass, seq) - - -class TestMassTolerances(unittest.TestCase): - """Testing the mass tolerance calculations in various scenarios.""" - - def test_mass_tol_with_ppm(self): - """Test get_min_max_mass with a user defined ppm measure.""" - window = fragments.get_min_max_mass( - mass_analyzer="FTMS", mass=10.0, mass_tolerance=15, unit_mass_tolerance="ppm" - ) - self.assertEqual(window, (9.99985, 10.00015)) - - def test_mass_tol_with_da(self): - """Test get_min_max_mass with a user defined da measure.""" - window = fragments.get_min_max_mass( - mass_analyzer="FTMS", mass=10.0, mass_tolerance=0.3, unit_mass_tolerance="da" - ) - self.assertEqual(window, (9.7, 10.3)) - - def test_mass_tol_with_defaults(self): - """Test get_min_max_mass with mass analyzer defaults.""" - window_ftms = fragments.get_min_max_mass(mass_analyzer="FTMS", mass=10.0) - window_itms = fragments.get_min_max_mass(mass_analyzer="ITMS", mass=10.0) - window_tof = fragments.get_min_max_mass(mass_analyzer="TOF", mass=10.0) - - self.assertEqual(window_ftms, (9.9998, 10.0002)) - self.assertEqual(window_tof, (9.9996, 10.0004)) - self.assertEqual(window_itms, (9.65, 10.35)) - - class TestInitializePeaks(unittest.TestCase): """Class to test initialize_peaks function.""" - def test_initialize_peaks(self): - """Test initialize_peaks with basic input.""" - fragments_input = {"sequence": "AAAA", "mass_analyzer": "FTMS", "charge": 3, "noncl_xl": False} + def _test_outputs(self, expected_input_file: Path, fragmentation_method: str): - with open(Path(__file__).parent / "data/fragments_meta_data.json") as file: + with open(expected_input_file) as file: expected_list_out = json.load(file) + expected_tmt_nt_term = 1 - expected_peptide_sequence = "AAAA" - expected_mass_s = 302.15902 + expected_peptide_sequence = "PEPTIDE" + expected_mass_s = 799.3599646700001 actual_list_out, actual_tmt_n_term, actual_peptide_sequence, actual_calc_mass_s = fragments.initialize_peaks( - **fragments_input + sequence="PEPTIDE", + mass_analyzer="FTMS", + charge=3, + fragmentation_method=fragmentation_method, ) self.assertEqual(actual_list_out, expected_list_out) @@ -131,56 +31,91 @@ def test_initialize_peaks(self): self.assertEqual(actual_peptide_sequence, expected_peptide_sequence) assert_almost_equal(actual_calc_mass_s, expected_mass_s, decimal=5) - def test_initialize_peaks_non_cl_xl(self): - """Test initialize_peaks_xl with basic input for non-cleavable crosslinked peptides.""" - initialize_peaks_xl_input = { - "sequence": "AKC", - "mass_analyzer": "FTMS", - "crosslinker_position": 2, - "crosslinker_type": "BS3", - "sequence_beta": "AKA", - } + def test_initialize_peaks_hcd_cid(self): + """Test initialize_peaks for HCD / CID input.""" + self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_hcd_cid.json", "HCD") + self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_hcd_cid.json", "CID") + + def test_initialize_peaks_etd_ecd(self): + """Test initialize_peaks for ETD / ECD input.""" + self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_etd_ecd.json", "ETD") + self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_etd_ecd.json", "ECD") + + def test_initialize_peaks_ethcd_etcid(self): + """Test initialize_peaks for ETCID / ETHCD input.""" + self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_ethcd_etcid.json", "ETHCD") + self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_ethcd_etcid.json", "ETCID") + + def test_initialize_peaks_uvpd(self): + """Test initialize_peaks with basic input, but for all six ion types for UVPD.""" + self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_uvpd.json", "UVPD") + + def _test_xl_outputs(self, expected_input_file: Path, **fragments_input): + + with open(expected_input_file) as file: + expected_list_out = json.load(file) - with open(Path(__file__).parent / "data/fragments_meta_data_non_cl_xl.json") as file: - expected_fragments_meta_data = json.load(file) expected_tmt_nt_term = 1 - expected_peptide_sequence = "AKC" - expected_mass = 320.15182 + expected_peptide_sequence = "PEKTIDE" + expected_mass = 830.40216367 ( actual_fragments_meta_data, actual_tmt_n_term, actual_peptide_sequence, actual_mass, - ) = fragments.initialize_peaks_xl(**initialize_peaks_xl_input) - self.assertEqual(actual_fragments_meta_data, expected_fragments_meta_data) + ) = fragments.initialize_peaks_xl(**fragments_input) + + self.assertEqual(actual_fragments_meta_data, expected_list_out) self.assertEqual(actual_tmt_n_term, expected_tmt_nt_term) self.assertEqual(actual_peptide_sequence, expected_peptide_sequence) assert_almost_equal(actual_mass, expected_mass, decimal=5) + def test_initialize_peaks_non_cl_xl(self): + """Test initialize_peaks_xl with basic input for non-cleavable crosslinked peptides.""" + initialize_peaks_xl_input = { + "sequence": "PEK[UNIMOD:1898]TIDE", + "mass_analyzer": "FTMS", + "crosslinker_position": 3, + "crosslinker_type": "BS3", + "sequence_beta": "AK[UNIMOD:1898]AT", + } + self._test_xl_outputs( + Path(__file__).parent / "data/fragments_meta_data_non_cl_xl.json", **initialize_peaks_xl_input + ) + def test_initialize_peaks_cl_xl(self): """Test initialize_peaks_xl with basic input for cleavable crosslinked peptides.""" initialize_peaks_xl_input = { - "sequence": "AKC", + "sequence": "PEK[UNIMOD:1896]TIDE", "mass_analyzer": "FTMS", - "crosslinker_position": 2, + "crosslinker_position": 3, "crosslinker_type": "DSSO", - "sequence_beta": "AKA", } + self._test_xl_outputs( + Path(__file__).parent / "data/fragments_meta_data_cl_xl.json", **initialize_peaks_xl_input + ) - with open(Path(__file__).parent / "data/fragments_meta_data_cl_xl.json") as file: - expected_fragments_meta_data = json.load(file) - expected_tmt_nt_term = 1 - expected_peptide_sequence = "AKC" - expected_mass = 320.15182 - ( - actual_fragments_meta_data, - actual_tmt_n_term, - actual_peptide_sequence, - actual_mass, - ) = fragments.initialize_peaks_xl(**initialize_peaks_xl_input) - self.assertEqual(actual_fragments_meta_data, expected_fragments_meta_data) - self.assertEqual(actual_tmt_n_term, expected_tmt_nt_term) - self.assertEqual(actual_peptide_sequence, expected_peptide_sequence) - assert_almost_equal(actual_mass, expected_mass, decimal=5) +class TestFragmentationMethod(unittest.TestCase): + """Class to test the retrieving of the IonTypes.""" + + def test_get_ion_types_hcd(self): + """Test retrieving ion types for HCD.""" + assert fragments.retrieve_ion_types("HCD") == ["y", "b"] + + def test_get_ion_types_etd(self): + """Test retrieving ion types for ETD.""" + assert fragments.retrieve_ion_types("ETD") == ["z", "c"] + + def test_get_ion_types_etcid(self): + """Test retrieving ion types for ETCID.""" + assert fragments.retrieve_ion_types("ETCID") == ["y", "z", "b", "c"] + + def test_get_ion_types_lower_case(self): + """Test lower case fragmentation method.""" + assert fragments.retrieve_ion_types("uvpd") == ["x", "y", "z", "a", "b", "c"] + + def test_invalid_fragmentation_method(self): + """Test if error is raised for invalid fragmentation method.""" + self.assertRaises(ValueError, fragments.retrieve_ion_types, "XYZ")