added value error and test for permute_seq_by_k

akita_utils/dna_utils.py

@@ -175,7 +175,9 @@ def permute_seq_k(seq_1hot, k=2):
     seq_length = len(seq_1hot)
     if seq_length % k != 0:
         raise ValueError("Sequence length must be divisible by k")
-
+    if seq_length < k:
+        raise ValueError("Sequence length must be greater than k")
+
     seq_1hot_perm = np.zeros_like(seq_1hot)
 
     num_permutations = seq_length // k

tests/test_dna_utils.py

@@ -1,4 +1,5 @@
-from akita_utils.dna_utils import dna_1hot, dna_1hot_to_seq, dna_seq_rc
+import numpy as np
+from akita_utils.dna_utils import dna_1hot, dna_1hot_to_seq, dna_seq_rc, test_permute_seq_k
 
 
 def test_dna_1hot_to_seq():
@@ -9,3 +10,46 @@ def test_dna_seq_rc():
     seq = "ACTG"
     rc_seq = "CAGT"
     assert dna_seq_rc(seq) == rc_seq
+
+
+def test_permute_seq_k():
+    # Test 1: Basic functionality
+    seq_1hot = np.array([[1, 0, 0, 0], 
+                         [0, 1, 0, 0], 
+                         [0, 0, 1, 0], 
+                         [0, 0, 0, 1], 
+                         [1, 0, 0, 0], 
+                         [0, 1, 0, 0]])
+    k = 2
+    result = permute_seq_k(seq_1hot, k)
+    assert result.shape == seq_1hot.shape, "Shape mismatch"
+    assert not np.array_equal(result, seq_1hot), "Permutation did not change sequence"
+
+    # Check that the sequence is a permutation of k-mers
+    permuted_k_mers = [result[i:i + k] for i in range(0, len(result), k)]
+    original_k_mers = [seq_1hot[i:i + k] for i in range(0, len(seq_1hot), k)]
+    assert sorted(map(tuple, original_k_mers)) == sorted(map(tuple, permuted_k_mers)), "Permuted k-mers are not as expected"
+
+    # Test 2: Edge case where sequence length is not divisible by k
+    try:
+        permute_seq_k(seq_1hot, k=3)
+    except ValueError as e:
+        assert str(e) == "Sequence length must be divisible by k", "Incorrect error message for length not divisible by k"
+
+    # Test 3: Edge case where k > sequence length
+    short_seq_1hot = np.array([[1, 0, 0, 0], 
+                               [0, 1, 0, 0]])
+    k_large = 3
+    try:
+        permute_seq_k(short_seq_1hot, k=k_large)
+    except ValueError as e:
+        assert str(e) == "Sequence length must be divisible by k", "Incorrect error message for k > sequence length"
+
+    # Test 4: Randomness check (manual validation needed)
+    np.random.seed(0)  # For reproducibility
+    result1 = permute_seq_k(seq_1hot, k)
+    np.random.seed(0)  # Reset seed to verify same permutation
+    result2 = permute_seq_k(seq_1hot, k)
+    assert np.array_equal(result1, result2), "Results should be consistent with the same seed"
+
+    print("All tests passed!")