closer to working in circular molecules

Author: manulera

dummy.py

@@ -31,6 +31,11 @@
     print("==")
     cutsite_pairs = new_seq.get_cutsite_pairs(new_seq.get_ds_meltsites(3))
 
+    print(repr(new_seq))
+    expected_product = new_seq.apply_cut(((10, 6), None), ((4, 4), None))
+    print(repr(expected_product))
+    break
+
     print(cutsite_pairs)
     print(new_seq.shift_melt_cutsite_pairs(cutsite_pairs))
     print(repr(new_seq))

dummy2.py

@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+from pydna.dseq import Dseq
+
+seq = Dseq("AGEEGaGJJJg", circular=True)
+
+cutsite_pairs = seq.get_cutsite_pairs(seq.get_ds_meltsites(3))
+
+shifted_cutsite_pairs = seq.shift_melt_cutsite_pairs(cutsite_pairs)
+
+print(cutsite_pairs)
+print(shifted_cutsite_pairs)
+assert shifted_cutsite_pairs == [((10, 6), None), ((7, 5), None)]
+
+expected_product = seq.apply_cut(((10, 6), None), ((7, 5), None), allow_overlap=True)

src/pydna/dseq.py

@@ -2698,7 +2698,9 @@ def shed_ss_dna(
 
         return Dseq.quick(new), strands
 
-    def apply_cut(self, left_cut: CutSiteType, right_cut: CutSiteType) -> "Dseq":
+    def apply_cut(
+        self, left_cut: CutSiteType, right_cut: CutSiteType, allow_overlap: bool = False
+    ) -> "Dseq":
         """Extracts a subfragment of the sequence between two cuts.
 
         For more detail see the documentation of get_cutsite_pairs.
@@ -2753,11 +2755,13 @@ def apply_cut(self, left_cut: CutSiteType, right_cut: CutSiteType) -> "Dseq":
             GttCTTAA
 
         """
-        if cuts_overlap(left_cut, right_cut, len(self)):
+
+        if not allow_overlap and cuts_overlap(left_cut, right_cut, len(self)):
             raise ValueError("Cuts by {} {} overlap.".format(left_cut[1], right_cut[1]))
 
         left_watson, left_crick, ovhg_left = self.get_cut_parameters(left_cut, True)
         right_watson, right_crick, _ = self.get_cut_parameters(right_cut, False)
+
         return Dseq(
             self[left_watson:right_watson]._data.translate(dscode_to_watson_table),
             self[left_crick:right_crick]