fixed bug that produced wrong overhang in linear, non-directional, single cut reactions.

Author: TimothyStiles

clone/clone.go

@@ -188,7 +188,15 @@ func CutWithEnzyme(part Part, directional bool, enzyme Enzyme) []Fragment {
 		// In the case of a single cut in a linear sequence, we get two fragments with only 1 stick end
 		fragmentSequence1 := sequence[overhangs[0].Position+overhangs[0].Length:]
 		fragmentSequence2 := sequence[:overhangs[0].Position]
-		overhangSequence := sequence[overhangs[0].Position : overhangs[0].Position+overhangs[0].Length]
+
+		var overhangSequence string
+
+		if len(forwardOverhangs) > 0 {
+			overhangSequence = sequence[overhangs[0].Position : overhangs[0].Position+overhangs[0].Length]
+		} else {
+			overhangSequence = sequence[overhangs[0].Position-overhangs[0].Length : overhangs[0].Position]
+		}
+
 		fragments = append(fragments, Fragment{fragmentSequence1, overhangSequence, ""})
 		fragments = append(fragments, Fragment{fragmentSequence2, "", overhangSequence})
 		return fragments

clone/clone_test.go

@@ -96,6 +96,44 @@ func TestCutWithEnzyme(t *testing.T) {
 	}
 }
 
+func TestCutWithEnzymeRegression(t *testing.T) {
+	sequence := "AGCTGCTGTTTAAAGCTATTACTTTGAGACC" // this is a real sequence I came across that was causing problems
+
+	part := Part{sequence, false}
+
+	// get enzymes with enzyme manager
+	enzymeManager := NewEnzymeManager(GetBaseRestrictionEnzymes())
+	bsa1, err := enzymeManager.GetEnzymeByName("BsaI")
+	if err != nil {
+		t.Errorf("Error when getting Enzyme. Got error: %s", err)
+	}
+
+	// cut with BsaI
+	fragments := CutWithEnzyme(part, false, bsa1)
+
+	// check that the fragments are correct
+	if len(fragments) != 2 {
+		t.Errorf("Expected 2 fragments, got: %d", len(fragments))
+	}
+
+	if fragments[0].ForwardOverhang != "ACTT" {
+		t.Errorf("Expected forward overhang to be ACTT, got: %s", fragments[0].ForwardOverhang)
+	}
+
+	if fragments[0].ReverseOverhang != "" {
+		t.Errorf("Expected reverse overhang to be GAGT, got: %s", fragments[0].ReverseOverhang)
+	}
+
+	if fragments[1].ForwardOverhang != "" {
+		t.Errorf("Expected forward overhang to be empty, got: %s", fragments[1].ForwardOverhang)
+	}
+
+	if fragments[1].ReverseOverhang != "ACTT" {
+		t.Errorf("Expected reverse overhang to be GAGT, got: %s", fragments[1].ReverseOverhang)
+	}
+
+}
+
 func TestCircularLigate(t *testing.T) {
 	// The following tests for complementing overhangs. Specific, this line:
 	// newSeed := Fragment{seedFragment.Sequence + seedFragment.ReverseOverhang + ReverseComplement(newFragment.Sequence), seedFragment.ForwardOverhang, ReverseComplement(newFragment.ForwardOverhang)}