simplify modification_mapping

MannLabs · Nov 12, 2024 · a9c2d46 · a9c2d46
1 parent 22f17d9
commit a9c2d46
Show file tree

Hide file tree

Showing 5 changed files with 9 additions and 12 deletions.
diff --git a/alphabase/psm_reader/maxquant_reader.py b/alphabase/psm_reader/maxquant_reader.py
@@ -1,4 +1,5 @@
 import copy
+from typing import Optional
 
 import numba
 import numpy as np
@@ -191,7 +192,7 @@ def _init_modification_mapping(self):
             psm_reader_yaml["maxquant"]["modification_mapping"]
         )
 
-    def set_modification_mapping(self, modification_mapping: dict):
+    def set_modification_mapping(self, modification_mapping: Optional[dict] = None):
         super().set_modification_mapping(modification_mapping)
         self._add_all_unimod()
         self._extend_mod_brackets()

diff --git a/alphabase/psm_reader/msfragger_reader.py b/alphabase/psm_reader/msfragger_reader.py
@@ -115,9 +115,6 @@ def __init__(
     def _init_column_mapping(self):
         self.column_mapping = psm_reader_yaml["msfragger_pepxml"]["column_mapping"]
 
-    def _init_modification_mapping(self):
-        self.modification_mapping = {}
-
     def _translate_modifications(self):
         pass
 

diff --git a/alphabase/psm_reader/pfind_reader.py b/alphabase/psm_reader/pfind_reader.py
@@ -104,9 +104,6 @@ def __init__(
     def _init_column_mapping(self):
         self.column_mapping = psm_reader_yaml["pfind"]["column_mapping"]
 
-    def _init_modification_mapping(self):
-        self.modification_mapping = {}
-
     def _translate_modifications(self):
         pass
 

diff --git a/alphabase/psm_reader/psm_reader.py b/alphabase/psm_reader/psm_reader.py
@@ -1,6 +1,7 @@
 import copy
 import os
 import warnings
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -153,7 +154,10 @@ def __init__(
             Defaults to False.
         """
 
-        self.set_modification_mapping(None)
+        self.modification_mapping = None
+        self.rev_mod_mapping = None
+
+        self.set_modification_mapping()
         self.add_modification_mapping(modification_mapping)
 
         if column_mapping is not None:
@@ -210,7 +214,7 @@ def add_modification_mapping(self, modification_mapping: dict):
 
         self.set_modification_mapping(self.modification_mapping)
 
-    def set_modification_mapping(self, modification_mapping: dict):
+    def set_modification_mapping(self, modification_mapping: Optional[dict] = None):
         if modification_mapping is None:
             self._init_modification_mapping()
         elif isinstance(modification_mapping, str):
@@ -224,6 +228,7 @@ def set_modification_mapping(self, modification_mapping: dict):
                 )
         else:
             self.modification_mapping = copy.deepcopy(modification_mapping)
+
         self._mods_as_lists()
         self._reverse_mod_mapping()
 

diff --git a/alphabase/psm_reader/sage_reader.py b/alphabase/psm_reader/sage_reader.py
@@ -593,9 +593,6 @@ def __init__(
     def _init_column_mapping(self):
         self.column_mapping = psm_reader_yaml["sage"]["column_mapping"]
 
-    def _init_modification_mapping(self):
-        self.modification_mapping = {}
-
     def _load_file(self, filename):
         raise NotImplementedError