closes #160

src/pydna/dseqrecord.py

@@ -893,7 +893,12 @@ def __getitem__(self, sl):
             answer.features = super().__getitem__(sl).features
         elif self.circular and sl_start > sl_stop:
             answer.features = self.shifted(sl_start).features
-            answer.features = [f for f in answer.features if f.location.parts[-1].end <= answer.seq.length]
+            # 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
+            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)]
         else:
             answer = Dseqrecord("")
         identifier = "part_{id}".format(id=self.id)

tests/test_module_dseqrecord.py

@@ -1850,6 +1850,7 @@ def test__repr_pretty_():
 
 def test___getitem__():
     from pydna.dseqrecord import Dseqrecord
+    from Bio.SeqFeature import SeqFeature, SimpleLocation
 
     s = Dseqrecord("GGATCC", circular=False)
     assert s[1:-1].seq == Dseqrecord("GATC", circular=False).seq
@@ -1868,6 +1869,19 @@ def test___getitem__():
     assert t[9:10].seq == Dseqrecord("").seq
     assert t[10:9].seq == Dseqrecord("").seq
 
+    # Test how slicing works with features (using sequence as in test_features_change_ori)
+    seqRecord = Dseqrecord("aaagGTACCTTTGGATCcggg", circular=True)
+    f1 = SeqFeature(SimpleLocation(4, 17), type="misc_feature", strand=1)
+    f2 = SeqFeature(SimpleLocation(17, 21, 1) + SimpleLocation(0, 4), type="misc_feature", strand=1)
+    seqRecord.features = [f1, f2]
+
+    # Exact feature sliced for normal and origin-spanning features
+    assert len(seqRecord[4:17].features) == 1
+    assert len(seqRecord[17:4].features) == 1
+
+    # Partial feature sliced for normal and origin-spanning features
+    assert len(seqRecord[2:20].features) == 1
+    assert len(seqRecord[13:8].features) == 1
 
 def test___eq__():
     from pydna.dseqrecord import Dseqrecord