Merge pull request #24 from wilhelm-lab/main

Merge main back in development

spectrum_fundamentals/fragments.py

@@ -70,9 +70,7 @@ def compute_peptide_mass(sequence: str) -> float:
     Compute the theoretical mass of the peptide sequence.
 
     :param sequence: Modified peptide sequence
-
     :raises AssertionError: if an unknown modification has been found in the peptide sequence
-
     :return: Theoretical mass of the sequence
     """
     peptide_sequence = sequence
@@ -115,7 +113,6 @@ def initialize_peaks(sequence: str, mass_analyzer: str, charge: int) -> Tuple[Li
     :param sequence: Modified peptide sequence
     :param mass_analyzer: Type of mass analyzer used eg. FTMS, ITMS
     :param charge: Precursor charge
-
     :raises AssertionError:  if peptide sequence contained an unknown modification. TODO do this within the get_mod func.
     :return: List of theoretical peaks, Flag to indicate if there is a tmt on n-terminus, Un modified peptide sequence
     """
@@ -212,6 +209,7 @@ def compute_ion_masses(seq_int: List[int], charge_onehot: List[int], tmt: str =
     Collects an integer sequence e.g. [1,2,3] with charge 2 and returns array with 174 positions for ion masses.
 
     Invalid masses are set to -1.
+
     :param seq_int: TODO
     :param charge_onehot: is a onehot representation of charge with 6 elems for charges 1 to 6
     :param tmt: TODO

spectrum_fundamentals/metrics/percolator.py

@@ -158,7 +158,6 @@ def get_delta_score(scores_df: pd.DataFrame, scoring_feature: str) -> np.ndarray
         The lowest scoring PSM of each group receives a delta score of 0.
         :param scores_df: must contain two columns: scoring_feature (eg. 'spectral_angle') and 'ScanNr'
         :param scoring_feature: feature name to get the delta scores of
-
         :raises NotImplementedError: If there is only one unique value for ScanNr in the scores_df.
         :return: numpy array of delta scores
         """