add

mrdna/readers/segmentmodel_from_cadnano.py

@@ -158,7 +158,7 @@ def gen_id_series(strand,part):
     
     return [pd.Series(df.loc[i]) for i in df.index]
 
-def gen_prop_table(part,seq_file=None,fill_seq="T"):
+def gen_prop_table(part):
     strand_set=[]
     for i in part.getidNums():
         fwd,rev=part.getStrandSets(i)
@@ -197,16 +197,6 @@ def gen_prop_table(part,seq_file=None,fill_seq="T"):
             nt_prop["bp"][bp2]=bp1
         except:
             pass
-    if seq_file is not None:
-        #under construction
-        seq=open(seq_file,"r")
-        for seqline in seq:
-            try:
-                int(seqline[0])
-            except:
-                continue
-
-
     return nt_prop
 
 
@@ -214,9 +204,9 @@ def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
     json_data=read_json_file(json_file)
     part,decoder=cadnano_parts(json_data)
     if decoder==2:
-        nt_prop=gen_prop_table_cad2(json_data,part)
+        nt_prop=gen_prop_table(part)
     elif decoder==3:
-        nt_prop=gen_prop_table_cad3(json_data,part)
+        nt_prop=gen_prop_table(part)
 
     if seq is None:
         if nt_prop["seq"][0]==-1:
@@ -229,5 +219,5 @@ def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
     three_prime=np.array((list(nt_prop["threeprime"])))
     stack=np.array((list(nt_prop["stack"])))
     orientation=np.array(list(nt_prop["orientation"]))
-    model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation=None, **model_parameters )
+    model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
     return model