update cadnano

mrdna/readers/__init__.py

@@ -9,6 +9,8 @@ def read_cadnano(json_file, sequence=None, fill_sequence='T', **model_parameters
 
 def read_cadnano_input(json_file,sequence=None,**model_parameters):
     from .segmentmodel_from_cadnano import mrdna_model_from_cadnano
+    from .segmentmodel_from_lists import model_from_basepair_stack_3prime
+    
 
     return mrdna_model_from_cadnano(json_file,seq=sequence,**model_parameters)
 

mrdna/readers/segmentmodel_from_cadnano.py

@@ -186,5 +186,10 @@ def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
             seq=None
         else:
             seq=nt_prop["seq"]
-    model = model_from_basepair_stack_3prime( nt_prop["r"], nt_prop["bp"], nt_prop["stack"], nt_prop["threeprime"], seq,nt_prop["orientation"], **model_parameters )
- 
+    
+    r=np.array(list(nt_prop['r']))
+    bp=np.array(list(nt_prop['bp']))
+    three_prime=np.array((list(nt_prop["threeprime"])))
+    orientation=np.array(list(nt_prop["orientation"]))
+    model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
+    return model