closes #161

pydna-group · Jan 30, 2024 · 28da1d8 · 28da1d8
1 parent bc13e92
commit 28da1d8
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Showing 3 changed files with 27 additions and 5 deletions.
diff --git a/src/pydna/dseqrecord.py b/src/pydna/dseqrecord.py
@@ -904,6 +904,9 @@ def __getitem__(self, sl):
             answer.features = [f for f in answer.features if (
                                _location_boundaries(f.location)[1] <= answer.seq.length and
                                _location_boundaries(f.location)[0] <= _location_boundaries(f.location)[1])]
+        elif self.circular and sl_start == sl_stop:
+            cut = ((sl_start, 0), None)
+            return self.apply_cut(cut, cut)
         else:
             answer = Dseqrecord("")
         identifier = "part_{id}".format(id=self.id)

diff --git a/tests/test_module_dseq.py b/tests/test_module_dseq.py
@@ -610,6 +610,12 @@ def test_Dseq___getitem__():
     assert s[9:1] == Dseq("")
     assert t[9:1] == Dseq("")
 
+    # Indexing of full circular molecule (https://github.com/BjornFJohansson/pydna/issues/161)
+    s = Dseq("GGATCC", circular=True)
+    str_seq = str(s)
+    for shift in range(len(s)):
+        assert str(s[shift : shift]) == str_seq[shift:] + str_seq[:shift]
+
 
 def test_cut_circular():
     from pydna.dseq import Dseq
@@ -890,16 +896,23 @@ def test_apply_cut():
         if start < 0:
             start += len(seq)
         # Cut with negative ovhg
-        new_cut = (( start, -3), None)
+        new_cut = ((start, -3), None)
         out = seq_shifted.apply_cut(new_cut, new_cut)
         assert str(out) == 'ATGaattacgtATG'
 
         # Cut with positive ovhg
         start = (start + 3) % len(seq)
-        new_cut = (( start, 3), None)
+        new_cut = ((start, 3), None)
         out = seq_shifted.apply_cut(new_cut, new_cut)
         assert str(out) == 'ATGaattacgtATG'
 
+        # A blunt cut
+        start = 4 - shift
+        new_cut = ((start, 0), None)
+        out = seq_shifted.apply_cut(new_cut, new_cut)
+        assert str(out) == 'ATGaattacgt'
+
+
 def test_cutsite_is_valid():
 
     from pydna.dseq import Dseq

diff --git a/tests/test_module_dseqrecord.py b/tests/test_module_dseqrecord.py
@@ -1867,7 +1867,7 @@ def test___getitem__():
     assert s[1:5].seq == Dseqrecord("GATC", circular=False).seq
     assert s[5:1:-1].seq == Dseqrecord("CCTA", circular=False).seq
 
-    assert t[1:1].seq == Dseqrecord("").seq
+    assert t[1:1].seq == Dseqrecord("GATCCG").seq
     assert t[5:1].seq == Dseqrecord("CG", circular=False).seq
     assert t[9:1].seq == Dseqrecord("").seq
     assert t[1:9].seq == Dseqrecord("").seq
@@ -1876,8 +1876,8 @@ def test___getitem__():
 
     # 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)
+    f1 = SeqFeature(SimpleLocation(4, 17, 1), type="misc_feature")
+    f2 = SeqFeature(SimpleLocation(17, 21, 1) + SimpleLocation(0, 4, 1), type="misc_feature")
     seqRecord.features = [f1, f2]
 
     # Exact feature sliced for normal and origin-spanning features
@@ -1888,6 +1888,12 @@ def test___getitem__():
     assert len(seqRecord[2:20].features) == 1
     assert len(seqRecord[13:8].features) == 1
 
+    # Indexing of full circular molecule (https://github.com/BjornFJohansson/pydna/issues/161)
+    s = Dseqrecord("GGATCC", circular=True)
+    str_seq = str(s.seq)
+    for shift in range(len(s)):
+        assert str(s[shift : shift].seq) == str_seq[shift:] + str_seq[:shift]
+
 def test___eq__():
     from pydna.dseqrecord import Dseqrecord