Fixed sequence assignment in segmentmodel_from_lists

mrdna/readers/segmentmodel_from_lists.py

@@ -290,9 +290,9 @@ def model_from_basepair_stack_3prime(coordinates, basepair, stack, three_prime,
     ## Assign sequence
     if sequence is not None:
         for hid in range(len(allSegments)):
-            resids = np.sort(np.where( (hmap==hid)*(fwd==1) )[0])
+            resids = np.where( (hmap==hid)*(fwd==1) )[0]
             s = allSegments[hid]
-            s.sequence = [sequence[r] for r in resids]
+            s.sequence = [sequence[r] for r in sorted(resids,key=lambda x: hrank[x])]
 
     ## Build model
     model = SegmentModel( allSegments,