refactor MSFraggerReader

alphabase/psm_reader/modification_mapper.py

@@ -95,8 +95,8 @@ def set_modification_mapping(
         ----------
         modification_mapping:
             If dictionary: the current modification_mapping will be overwritten by this.
-            If str: the parameter will be interpreted as a reader type, and the modification_mapping is read from the
-                "modification_mapping" section of the psm_reader_yaml
+            If str: the parameter will be interpreted as a modification_mapping_type, and the mapping is read from the
+                respective key in the "modification_mappings" section of the psm_reader_yaml
 
         """
         if modification_mapping is None:

alphabase/psm_reader/msfragger_reader.py

@@ -21,12 +21,11 @@ def _is_fragger_decoy(proteins: List[str]) -> bool:
     return all(prot.lower().startswith("rev_") for prot in proteins)
 
 
-mass_mapped_mods = psm_reader_yaml["msfragger_pepxml"]["mass_mapped_mods"]
-mod_mass_tol = psm_reader_yaml["msfragger_pepxml"]["mod_mass_tol"]
-
-
 def _get_mods_from_masses(  # noqa: PLR0912, C901 too many branches, too complex TODO: refactor
-    sequence: str, msf_aa_mods: List[str]
+    sequence: str,
+    msf_aa_mods: List[str],
+    mass_mapped_mods: List[str],
+    mod_mass_tol: float,
 ) -> Tuple[str, str, str, str]:
     mods = []
     mod_sites = []
@@ -134,7 +133,10 @@ def __init__(  # noqa: PLR0913, D417 # too many arguments in function definition
             rt_unit=rt_unit,
             **kwargs,
         )
-        self.keep_unknown_aa_mass_diffs = keep_unknown_aa_mass_diffs
+        self._keep_unknown_aa_mass_diffs = keep_unknown_aa_mass_diffs
+        # TODO: should those be set via API, too?
+        self._mass_mapped_mods = psm_reader_yaml["msfragger_pepxml"]["mass_mapped_mods"]
+        self._mod_mass_tol = psm_reader_yaml["msfragger_pepxml"]["mod_mass_tol"]
 
     def _translate_modifications(self) -> None:
         pass
@@ -183,11 +185,16 @@ def _load_modifications(self, origin_df: pd.DataFrame) -> None:
             self._psm_df[PsmDfCols.AA_MASS_DIFF_SITES],
         ) = zip(
             *origin_df[["peptide", "modifications"]].apply(
-                lambda x: _get_mods_from_masses(*x), axis=1
+                lambda x: _get_mods_from_masses(
+                    *x,
+                    mass_mapped_mods=self._mass_mapped_mods,
+                    mod_mass_tol=self._mod_mass_tol,
+                ),
+                axis=1,
             )
         )
 
-        if not self.keep_unknown_aa_mass_diffs:
+        if not self._keep_unknown_aa_mass_diffs:
             self._psm_df[PsmDfCols.TO_REMOVE] += (
                 self._psm_df[PsmDfCols.AA_MASS_DIFFS] != ""
             )