closes #195

src/pydna/dseqrecord.py

@@ -901,10 +901,9 @@ def __getitem__(self, sl):
             # origin-spanning features should only be included after shifting
             # in cases where the slice comprises the entire sequence, but then
             # sl_start == sl_stop and the second condition is not met
-            # TODO: _location_boundaries
             answer.features = [f for f in answer.features if (
-                               f.location.parts[-1].end <= answer.seq.length and
-                               f.location.parts[0].start <= f.location.parts[-1].end)]
+                               _location_boundaries(f.location)[1] <= answer.seq.length and
+                               _location_boundaries(f.location)[0] <= _location_boundaries(f.location)[1])]
         else:
             answer = Dseqrecord("")
         identifier = "part_{id}".format(id=self.id)
@@ -1362,7 +1361,8 @@ def apply_cut(self, left_cut, right_cut):
                 #     2222
                 #
                 left_watson, left_crick, left_ovhg = self.seq.get_cut_parameters(left_cut, True)
-                features = self.shifted(min(left_watson, left_crick)).features
+                initial_shift = left_watson if left_ovhg < 0 else left_crick
+                features = self.shifted(initial_shift).features
                 # for f in features:
                 #     print(f.id, f.location, _location_boundaries(f.location))
                 # Here, we have done what's shown below (* indicates the origin).

src/pydna/utils.py

@@ -50,21 +50,35 @@ def shift_location(original_location, shift, lim):
     """docstring."""
     newparts = []
     strand = original_location.strand
+
     for part in original_location.parts:
-        ns = (part.start + shift) % lim
-        ne = (part.end + shift) % lim or lim
-        oe = newparts[-1].end if newparts else None
+        new_start = (part.start + shift) % lim
+        new_end = (part.end + shift) % lim or lim
+        old_start, old_end = (newparts[-1].start, newparts[-1].end) if len(newparts) else (None, None)
+
+        # The "join with old" cases are for features with multiple parts
+        # in which consecutive parts do not have any bases between them.
+        # This type of feature is generated to represent a feature that
+        # spans the origin of a circular sequence. See more details in
+        # https://github.com/BjornFJohansson/pydna/issues/195
+
         if len(part) == 0:
-            newparts.append(_sl(ns, ns, strand))
+            newparts.append(_sl(new_start, new_start, strand))
             continue
-        elif oe == ns:
+        # Join with old, case 1
+        elif strand != -1 and old_end == new_start:
+            part = newparts.pop()
+            part._end = new_end
+            new_start = part.start
+        # Join with old, case 2
+        elif strand == -1 and old_start == new_end:
             part = newparts.pop()
-            part._end = ne
-            ns = part.start
-        if ns < ne:
-            newparts.append(_sl(ns, ne, strand))
+            part._start = new_start
+            new_end = part.end
+        if new_start < new_end:
+            newparts.append(_sl(new_start, new_end, strand))
         else:
-            parttuple = (_sl(ns, lim, strand), _sl(0, ne, strand))
+            parttuple = (_sl(new_start, lim, strand), _sl(0, new_end, strand))
             newparts.extend(parttuple if strand != -1 else parttuple[::-1])
     try:
         newloc = _cl(newparts)
@@ -836,8 +850,7 @@ def cuts_overlap(left_cut, right_cut, seq_len):
 
 def location_boundaries(loc: _Union[_sl,_cl]):
 
-    #TODO: pending on https://github.com/BjornFJohansson/pydna/pull/179
-    if loc.strand != 1:
+    if loc.strand == -1:
         return loc.parts[-1].start, loc.parts[0].end
     else:
         return loc.parts[0].start, loc.parts[-1].end

tests/test_module_utils.py

@@ -459,8 +459,15 @@ def close(self):
 
 def test_shift_location():
     from pydna.utils import shift_location
+    from Bio.SeqFeature import SimpleLocation
+
+    # TODO: more tests here
+
+    # Shifting of locations should be reversible (https://github.com/BjornFJohansson/pydna/issues/195)
+    for strand in (1, -1, None):
+        loc = SimpleLocation(0, 2, strand)
+        assert shift_location(shift_location(loc, 1, 6), -1, 6) == loc
 
-    # Shifting of locations should be reversible
 
 
 if __name__ == "__main__":