fix: rna2vec case-insensitivity for secondary structures

pyaptamer/utils/_rna.py

@@ -141,6 +141,7 @@ def rna2vec(
 
     result = []
     for sequence in sequence_list:
+        sequence = sequence.upper()  # ensure case-insensitivity
         # convert DNA to RNA only for RNA sequences
         if sequence_type == "rna":
             sequence = dna2rna(sequence)

pyaptamer/utils/tests/test_rna2vec_robustness.py

@@ -0,0 +1,19 @@
+import numpy as np
+
+from pyaptamer.utils import rna2vec
+
+
+def test_rna2vec_case_insensitivity():
+    """
+    Test that rna2vec handles secondary structures in a case-insensitive way.
+    Regression test for Issue where lowercase 'ss' inputs returned zero vectors.
+    """
+    sequences_upper = ["SSHH"]
+    sequences_lower = ["sshh"]
+
+    result_upper = rna2vec(sequences_upper, sequence_type="ss", max_sequence_length=10)
+    result_lower = rna2vec(sequences_lower, sequence_type="ss", max_sequence_length=10)
+
+    # Both should be identical and non-zero
+    assert np.array_equal(result_upper, result_lower)
+    assert np.any(result_upper != 0)