test: fix tests, allow for negative indices in slicing

Author: jcharkow

openms_python/py_aasequence.py

@@ -245,7 +245,7 @@ def __getitem__(self, index):
             # Handle negative indices
             if index < 0:
                 index = len(self) + index
-            if index < 0 or index >= len(self):
+            if index >= len(self):
                 raise IndexError(f"Index {index} out of range for sequence of length {len(self)}")
             residue = self._sequence.getResidue(index)
             residue_char = residue.getOneLetterCode()
@@ -394,10 +394,18 @@ def has_suffix(self, suffix: str) -> bool:
 
 
     # ===================== Exporting =======================
-    def to_string(self, modified=True, mod_format: Optional[Literal['unimod', 'bracket']] = 'unimod') -> str:
+    def to_string(self, modified=True, mod_format: Optional[Literal['default', 'unimod', 'bracket']] = 'default') -> str:
         """
         Get string representation of the sequence.
 
+        Args:
+            modified (bool): Whether to include modifications in the string.
+            mod_format (Optional[Literal['default', 'unimod', 'bracket']]): Format for modifications.
+                'default' for OpenMS format,
+                'unimod' for UniMod format,
+                'bracket' for bracket notation.
+                 Default is 'unimod'.                
+
         Returns:
             str: Amino acid sequence as string.
 
@@ -409,7 +417,9 @@ def to_string(self, modified=True, mod_format: Optional[Literal['unimod', 'brack
             return self.unmodified_sequence
 
         else:
-            if mod_format == 'unimod':
+            if mod_format == 'default':
+                return self._sequence.toString()
+            elif mod_format == 'unimod':
                 return self._sequence.toUniModString()
             elif mod_format == 'bracket':
                 return self._sequence.toBracketString()

tests/test_py_aasequence.py

@@ -118,25 +118,22 @@ def test_py_aasequence_iteration():
     seq = Py_AASequence.from_string("PEPTIDE")
     residues = list(seq)
 
-    assert residues == ["P", "E", "P", "T", "I", "D", "E"]
+    assert [res.sequence for res in residues] == ["P", "E", "P", "T", "I", "D", "E"]
     assert len(residues) == 7
 
 
 def test_py_aasequence_indexing():
     """Test indexing into sequence."""
     seq = Py_AASequence.from_string("PEPTIDE")
 
-    assert seq[0] == "P"
-    assert seq[1] == "E"
-    assert seq[6] == "E"
+    assert seq[0].sequence == "P"
+    assert seq[1].sequence == "E"
+    assert seq[6].sequence == "E"
 
     # Test out of bounds
     with pytest.raises(IndexError):
         _ = seq[7]
 
-    with pytest.raises(IndexError):
-        _ = seq[-1]
-
 
 def test_py_aasequence_string_representation():
     """Test string representations."""
@@ -258,3 +255,37 @@ def test_py_aasequence_with_native_aasequence():
 
     assert seq.sequence == "PEPTIDE"
     assert seq.native is native
+
+
+def test_py_aasequence_to_string():
+    """Test to_string method with different options."""
+    seq = Py_AASequence.from_string("PEPTIDEM(Oxidation)")
+
+    # Default should return modified string in default format
+    mod_str = seq.to_string()
+    assert mod_str == "PEPTIDEM(Oxidation)"
+
+    # Unmodified should return unmodified sequence
+    unmod_str = seq.to_string(modified=False)
+    assert unmod_str == "PEPTIDEM"
+
+    # Bracket format
+    bracket_str = seq.to_string(modified=True, mod_format='bracket')
+    assert bracket_str == "PEPTIDEM[147]"
+
+    # unimod format
+    unimod_str = seq.to_string(modified=True, mod_format='unimod')
+    assert unimod_str == "PEPTIDEM(UniMod:35)"
+
+    # Invalid format should raise error
+    with pytest.raises(ValueError):
+        _ = seq.to_string(modified=True, mod_format='invalid_format')
+
+
+def test_slicing():
+    aa_seq = Py_AASequence.from_string('PEPTIDEM(Oxidation)R')
+    assert aa_seq[0].sequence == 'P'
+    assert aa_seq[-1].sequence == 'R'
+    assert aa_seq[1:4].sequence == 'EPT'
+    assert aa_seq[-2:].sequence == 'M(Oxidation)R'
+