From 7d22e5fd7585192998f79d00f23b20c648e05172 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Wed, 22 Nov 2023 19:02:02 +0000
Subject: [PATCH] WIP

---
 src/pydna/dseq.py         | 9 +++++++--
 tests/test_module_dseq.py | 6 ++++++
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/pydna/dseq.py b/src/pydna/dseq.py
index 764c0265..703d436e 100644
--- a/src/pydna/dseq.py
+++ b/src/pydna/dseq.py
@@ -1482,9 +1482,12 @@ def apply_cut(self, left_cut, right_cut):
         left_watson, left_crick = left_cut[0]
         ovhg = 0 if left_cut[1] is None else left_cut[1].ovhg
         right_watson, right_crick = right_cut[0]
+        # TODO: this fills up nucleotides when it should not. It should either use the watson and crick
+        #      sequences as they are, or use the ovhg to shift the start or finish.
         return Dseq(
                     str(self[left_watson:right_watson]),
-                    _rc(str(self[left_crick:right_crick])),
+                    # The line below could be easier to understand as _rc(str(self[left_crick:right_crick])), but it does not preserve the case
+                    str(self.reverse_complement()[len(self) - right_crick:len(self) - left_crick]),
                     ovhg=ovhg,
                 )
 
@@ -1494,7 +1497,9 @@ def get_cutsite_pairs(self, cutsites):
         if len(cutsites) == 1 and self.circular:
             return [(cutsites[0], cutsites[0])]
         if not self.circular:
-            cutsites = [((0, 0), None), *cutsites, ((len(self), len(self)), None)]
+            left_edge = ((0 if self.ovhg < 0 else self.ovhg, 0 if self.ovhg < 0 else -self.ovhg), None)
+            right_edge = ((left_edge[0][0] + len(self.watson), left_edge[0][1] + len(self.crick)), None)
+            cutsites = [left_edge, *cutsites, right_edge]
         else:
             # Return in the same order as previous pydna versions
             cutsites = [cutsites[-1]] + cutsites[:-1]
diff --git a/tests/test_module_dseq.py b/tests/test_module_dseq.py
index 4851c3a0..34346458 100644
--- a/tests/test_module_dseq.py
+++ b/tests/test_module_dseq.py
@@ -442,6 +442,12 @@ def test_dseq():
     frag1 = Dseq("G", "gatcc", 0)
     frag2 = Dseq("GATCCaaa", "g", -4)
 
+    print(obj.__repr__())
+    print(obj.cut(BamHI)[0].__repr__())
+    print(frag1.__repr__())
+    print(obj.cut(BamHI)[1].__repr__())
+    print(frag2.__repr__())
+
     assert obj.cut(BamHI) == (frag1, frag2)
 
     assert frag1 + frag2 == obj