closes #279 again (for circular seqs)

pydna-group · Nov 7, 2024 · 7d03dd0 · 7d03dd0
1 parent 0a9fe6e
commit 7d03dd0
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diff --git a/src/pydna/amplify.py b/src/pydna/amplify.py
@@ -351,11 +351,13 @@ def products(self):
                     feats = self.template[
                         fp.position - fp._fp : rp.position + rp._fp
                     ].features  # Save features covered by primers
-                    shift_amount = len(fp.tail)
-                    feats = [_shift_feature(f, shift_amount, None) for f in feats]
                     tpl = self.template
                 else:
                     continue
+                # Shift features to the right if there was a tail
+                shift_amount = len(fp.tail)
+                feats = [_shift_feature(f, shift_amount, None) for f in feats]
+
                 if tpl.circular and fp.position == rp.position:
                     prd = _Dseqrecord(fp) + _Dseqrecord(rp).reverse_complement()
                 else:

diff --git a/tests/test_module_amplify.py b/tests/test_module_amplify.py
@@ -799,6 +799,11 @@ def test_annotation():
 
     assert pcr_product.features[0].location.extract(pcr_product).seq == dsr.seq
 
+    # Also works in circular sequences
+    dsr_circ = dsr.looped()
+    pcr_product_circ = pcr(forward_primer, reverse_primer, dsr_circ)
+    assert str(pcr_product_circ.features[0].location.extract(pcr_product_circ).seq) == str(dsr_circ.seq)
+
 
 if __name__ == "__main__":
     pytest.main([__file__, "-vv", "-s"])