Exposed fill_sequence in read_cadnano

mrdna/readers/__init__.py

 ## TODO: make module this package conform to a single style for input/output
 
-def read_cadnano(json_file, **model_parameters):
+def read_cadnano(json_file, sequence=None, fill_sequence='T', **model_parameters):
     from .cadnano_segments import read_json_file
     from .cadnano_segments import read_model as model_from_cadnano_json
 
     data = read_json_file(json_file)
-    return model_from_cadnano_json(data, **model_parameters)
+    return model_from_cadnano_json(data, sequence, fill_sequence, **model_parameters)
 
 def read_vhelix(maya_file, **model_parameters):
     from .polygon_mesh import parse_maya_file, convert_maya_bases_to_segment_model
-    from ..model.dna_sequence import m13 as m13seq
 
     maya_bases = parse_maya_file(maya_file)
     model = convert_maya_bases_to_segment_model( maya_bases, **model_parameters )

mrdna/readers/cadnano_segments.py

@@ -673,7 +673,7 @@ def _get_lattice(part):
 def package_archive( name, directory ):
     ...
 
-def read_model(json_data, sequence=None, **kwargs):
+def read_model(json_data, sequence=None, fill_sequence='T', **kwargs):
     """ Read in data """
     part = decode_cadnano_part(json_data)
     model = cadnano_part(part,
@@ -689,9 +689,9 @@ def read_model(json_data, sequence=None, **kwargs):
 
     if sequence is None or len(sequence) == 0:
         ## default m13mp18
-        model.set_sequence(m13seq,force=False)
+        model.set_sequence(m13seq,force=False, fill_sequence=fill_sequence)
     else:
-        model.set_sequence(sequence)
+        model.set_sequence(sequence, fill_sequence=fill_sequence)
 
     return model