WIP

dummy.py

@@ -0,0 +1,40 @@
+from pydna.dseqrecord import Dseqrecord
+from Bio.SeqFeature import SeqFeature, SimpleLocation
+from Bio.Restriction import EcoRI
+# _shift_location(SimpleLocation(x_start, x_start + length), 0, len(first)
+
+# seq = Dseqrecord("acgtTTTaatt", circular=True)
+# seq.features.append(SeqFeature(SimpleLocation(4, 7), id='full_overlap'))
+# seq.features.append(SeqFeature(SimpleLocation(3, 7), id='left_side'))
+# seq.features.append(SeqFeature(SimpleLocation(4, 8), id='right_side'))
+# # print(*seq.features, sep='\n')
+# print('===')
+# dummy_cut = ((4, 7), type('DynamicClass', (), {'ovhg': -3})())
+# open_seq = seq.apply_cut(dummy_cut, dummy_cut)
+
+# print(*open_seq.features, sep='\n')
+# print(open_seq.seq.__repr__())
+
+
+
+# opened = Dseqrecord('aaGAATTCaa', circular=True).cut(EcoRI)[0]
+
+
+
+# dummy = Dseqrecord('aaGAATTCaa', circular=False)
+
+# print(dummy)
+# print(dummy.apply_cut(None, None))
+
+
+def ranges_overlap(x, y):
+    return (x[1] > y[0]) != (y[1] < x[0])
+
+print(ranges_overlap((1, 2), (3, 4)))
+print(ranges_overlap((1, 3), (2, 4)))
+print(ranges_overlap((1, 4), (2, 3)))
+print(ranges_overlap((2, 3), (1, 4)))
+print(ranges_overlap((2, 4), (1, 3)))
+print(ranges_overlap((3, 4), (1, 2)))
+print(ranges_overlap((1, 2), (2, 3)))
+

src/pydna/dseq.py

@@ -1519,7 +1519,7 @@ def right_end_position(self) -> tuple[int, int]:
     def apply_cut(self, left_cut, right_cut):
 
         left_watson, left_crick = left_cut[0] if left_cut is not None else self.left_end_position()
-        ovhg = self.ovhg if left_cut is None else left_cut[1].ovhg
+        ovhg = left_cut[1].ovhg if left_cut is not None else self.ovhg
         right_watson, right_crick = right_cut[0] if right_cut is not None else self.right_end_position()
         return Dseq(
                     str(self[left_watson:right_watson]),

tests/test_module_dseq.py

@@ -838,5 +838,18 @@ def test_apply_cut():
     assert seq.apply_cut(None, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs('aaGAATT', watson_ovhg=-4, crick_ovhg=-1)
     assert seq.apply_cut(EcoRI_cut, None) == Dseq.from_full_sequence_and_overhangs('AATTCaa', watson_ovhg=-1, crick_ovhg=-4)
 
+    # A repeated cut in a circular molecule opens it up
+    seq = Dseq('aaGAATTCaa', circular=True)
+    assert seq.apply_cut(EcoRI_cut, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs('AATTCaaaaGAATT', watson_ovhg=-4, crick_ovhg=-4)
+
+    # Two cuts extract a subsequence
+    seq = Dseq('aaGAATTCaaGAATTCaa', circular=True)
+    EcoRI_cut_2 = ((11, 15), type('DynamicClass', (), {'ovhg': -4})())
+    assert seq.apply_cut(EcoRI_cut, EcoRI_cut_2) == Dseq.from_full_sequence_and_overhangs('AATTCaaGAATT', watson_ovhg=-4, crick_ovhg=-4)
+
+    # TODO: Overlapping cuts should return an error
+    EcoRI_cut_2 = ((4, 8), type('DynamicClass', (), {'ovhg': -4})())
+    assert seq.apply_cut(EcoRI_cut, EcoRI_cut_2)
+
 if __name__ == "__main__":
     pytest.main([__file__, "-vv", "-s"])