introduce modification_mapping_type

alphabase/constants/const_files/psm_reader.yaml

@@ -13,13 +13,8 @@ alphapept:
     'raw_name': 'raw_name' #parse from `ms_data.hdf`` file
     'fdr': 'q_value'
     'decoy': 'decoy'
-  modification_mapping:
-    'Carbamidomethyl@C': 'cC'
-    'Oxidation@M': 'oxM'
-    'Phospho@S': 'pS'
-    'Phospho@T': 'pT'
-    'Phospho@Y': 'pY'
-    'Acetyl@Protein_N-term': 'a'
+  modification_mapping_type: 'alphapept'
+
 
 maxquant:
   reader_type: maxquant
@@ -49,7 +44,10 @@ maxquant:
     'genes': ['Gene Names','Gene names']
     'decoy': 'Reverse'
     'intensity': 'Intensity'
-  modification_mapping:
+  modification_mapping_type: 'maxquant'
+
+modification_mappings:
+  maxquant:
     'Dimethyl@K':
       - 'K(Dimethyl)'
     'Dimethyl@R':
@@ -103,6 +101,13 @@ maxquant:
     'Deamidated@Q': ['Q(Deamidation (NQ))','Q(de)']
     'GlyGly@K': ['K(GlyGly (K))', 'K(gl)']
     'hydroxyisobutyryl@K': 'K(2-)'
+  alphapept:
+    'Carbamidomethyl@C': 'cC'
+    'Oxidation@M': 'oxM'
+    'Phospho@S': 'pS'
+    'Phospho@T': 'pT'
+    'Phospho@Y': 'pY'
+    'Acetyl@Protein_N-term': 'a'
 
 pfind:
   reader_type: pfind
@@ -119,6 +124,7 @@ pfind:
     'uniprot_ids': 'Proteins'
     'fdr': 'Q-value'
     'decoy': ['Target/Decoy', 'Targe/Decoy']
+  modification_mapping_type: 'maxquant'
 
 msfragger_pepxml:
   reader_type: msfragger_pepxml
@@ -146,6 +152,7 @@ msfragger_pepxml:
     - 'Dimethyl@K' # Any_N-term is not needed here as it will be infered in-the-fly
     - 'Methyl@E' #an example of a PTM that can be C-term
   mod_mass_tol: 0.1 # Da
+  modification_mapping_type: 'maxquant'
 
 diann:
   reader_type: diann
@@ -168,7 +175,7 @@ diann:
     'fdr': 'Q.Value'
   mod_seq_columns:
     - "Modified.Sequence"
-  modification_mapping: 'maxquant'
+  modification_mapping_type: 'maxquant'
 
 spectronaut_report:
   reader_type: spectronaut_report
@@ -184,7 +191,7 @@ spectronaut_report:
     'charge': 'charge'
   mod_seq_columns:
     - 'ModifiedSequence'
-  modification_mapping: 'maxquant'
+  modification_mapping_type: 'maxquant'
 
 spectronaut:
   reader_type: spectronaut
@@ -208,7 +215,7 @@ spectronaut:
     - 'ModifiedPeptideSequence'
     - 'LabeledSequence'
     - 'FullUniModPeptideName'
-  modification_mapping: 'maxquant'
+  modification_mapping_type: 'maxquant'
 
 library_reader_base:
   reader_type: library_reader_base
@@ -239,7 +246,7 @@ library_reader_base:
     - 'FullUniModPeptideName'
     - 'LabeledSequence'
     - 'FullUniModPeptideName'
-  modification_mapping: 'maxquant'
+  modification_mapping_type: 'maxquant'
 
 sage:
   reader_type: sage
@@ -258,3 +265,4 @@ sage:
     'peptide_fdr': 'peptide_q'
     'protein_fdr': 'protein_q'
     'decoy': 'is_decoy'
+  modification_mapping_type: 'maxquant'

alphabase/psm_reader/alphapept_reader.py

@@ -52,7 +52,6 @@ class AlphaPeptReader(PSMReaderBase):
     """Reader for AlphaPept's *.ms_data.hdf files."""
 
     _reader_type = "alphapept"
-    _modification_type = "alphapept"
 
     def _load_file(self, filename: str) -> pd.DataFrame:
         """Load an AlphaPept output file to a DataFrame."""

alphabase/psm_reader/maxquant_reader.py

@@ -128,7 +128,6 @@ class MaxQuantReader(PSMReaderBase):
 
     _reader_type = "maxquant"
     _add_unimod_to_mod_mapping = True
-    _modification_type = "maxquant"
 
     def __init__(  # noqa: PLR0913, D417 # too many arguments in function definition, missing argument descriptions
         self,

alphabase/psm_reader/modification_mapper.py

@@ -15,7 +15,7 @@ def __init__(
         custom_modification_mapping: Optional[Dict[str, str]],
         *,
         reader_yaml: Dict,
-        modification_type: Optional[str],
+        mapping_type: str,
         add_unimod_to_mod_mapping: bool,
     ):
         """Initialize the ModificationMapper.
@@ -35,7 +35,7 @@ def __init__(
         reader_yaml:
             the yaml (read from file) containing the modification mappings
 
-        modification_type:
+        mapping_type:
             the type of modification mapping ("maxquant" or "alphapept")
 
         add_unimod_to_mod_mapping:
@@ -44,7 +44,7 @@ def __init__(
         """
         self._psm_reader_yaml = reader_yaml
         self._add_unimod_to_mod_mapping = add_unimod_to_mod_mapping
-        self._modification_type = modification_type
+        self._mapping_type = mapping_type
 
         self.modification_mapping = None
         self.rev_mod_mapping = None
@@ -102,16 +102,13 @@ def set_modification_mapping(
         if modification_mapping is None:
             self._init_modification_mapping()
         elif isinstance(
-            modification_mapping, str
-        ):  # TODO: remove this overloading of the parameter by introducing yaml key "modification_mapping_type"
-            if modification_mapping in self._psm_reader_yaml:
-                self.modification_mapping = self._psm_reader_yaml[modification_mapping][
-                    "modification_mapping"
-                ]
-            else:
-                raise ValueError(
-                    f"Unknown modification mapping: {modification_mapping}"
-                )
+            modification_mapping,
+            str,  # interprete as modification_mapping_type
+        ):
+            self.modification_mapping = self._psm_reader_yaml["modification_mappings"][
+                modification_mapping
+            ]
+
         else:
             self.modification_mapping = copy.deepcopy(modification_mapping)
 
@@ -125,12 +122,9 @@ def set_modification_mapping(
 
     def _init_modification_mapping(self) -> None:
         """Initialize the modification mapping from the psm_reader_yaml or as an empty dictionary."""
-        if self._modification_type is not None:
-            self.modification_mapping = self._psm_reader_yaml[self._modification_type][
-                "modification_mapping"
-            ]
-        else:
-            self.modification_mapping = {}
+        self.modification_mapping = self._psm_reader_yaml["modification_mappings"][
+            self._mapping_type
+        ]
 
     def _add_all_unimod(self) -> None:
         """Add all unimod modifications to the modification mapping."""

alphabase/psm_reader/psm_reader.py

@@ -36,8 +36,6 @@ class PSMReaderBase(ABC):
     _reader_type: str
     # whether to add the unimod mappings to the modification mapping
     _add_unimod_to_mod_mapping: bool = False
-    # the typ of modification mapping to be used
-    _modification_type: Optional[str] = None
     # whether 'rt_norm' values in self._psm_dd will be normalized using min/max values
     #  Useful to normalize iRT values as they contain negative values.
     _min_max_rt_norm = False
@@ -127,9 +125,9 @@ def __init__(  # noqa: PLR0913 # too many arguments
         self._modification_mapper = ModificationMapper(
             modification_mapping,
             reader_yaml=copy.deepcopy(psm_reader_yaml),
-            modification_type=psm_reader_yaml[self._reader_type].get(
-                "modification_mapping_type", None
-            ),
+            mapping_type=psm_reader_yaml[self._reader_type][
+                "modification_mapping_type"
+            ],
             add_unimod_to_mod_mapping=self._add_unimod_to_mod_mapping,
         )
 

tests/integration/test_psm_readers.py

@@ -229,6 +229,8 @@ def _assert_reference_df_equal(
 def test_psm_reader_yaml() -> None:
     """Test that all column mappings in the psm_reader.yaml are covered by string constant keys."""
     for reader_config in psm_reader_yaml.values():
+        if reader_config == "modification_mappings":
+            continue
         ks = [k for k in reader_config["column_mapping"]]
         assert (
             set(ks) - set(PsmDfCols.get_values()) - set(LibPsmDfCols.get_values())