address ai comments

Author: jcharkow

openms_python/py_aasequence.py

@@ -4,6 +4,7 @@
 
 from typing import Optional, Literal
 import pyopenms as oms
+import warnings
 
 
 class Py_AASequence:
@@ -334,8 +335,9 @@ def __lt__(self, other: Py_AASequence) -> bool:
             return NotImplemented
         return self.sequence < other.sequence
     def count(self, residue: str) -> int:
-        """Count occurrences of a residue, to be consistent with str.count()."""
-        return self._sequence.count(residue)
+        """Count occurrences of a residue, to be consistent with str.count(), note currently does not account for modifications"""
+        warnings.warn("count method does not account for modifications")
+        return self.unmodified_sequence.count(residue)
 
     # ==================== Additional Utilities ====================
 

tests/test_py_aasequence.py

@@ -289,3 +289,9 @@ def test_slicing():
     assert aa_seq[1:4].sequence == 'EPT'
     assert aa_seq[-2:].sequence == 'M(Oxidation)R'
 
+def test_count():
+    aa_seq = Py_AASequence.from_string('PEPTIDEM(Oxidation)R')
+    assert aa_seq.count('E') == 2
+    assert aa_seq.count('P') == 2
+    assert aa_seq.count('K') == 0
+