Updated readers to more consistently read sequence

dnarbd/model/dna_sequence.py

@@ -8,6 +8,7 @@ def read_sequence_file(sequenceFile=_m13_path):
             l = l.strip().replace(" ", "")
             if l[0] in (";","#"): continue
             seq.extend([c.upper() for c in l])
-    return seq
+    return list(seq)
 
 m13 = read_sequence_file()
+

dnarbd/readers/__init__.py

@@ -6,6 +6,7 @@ from .cadnano_segments import read_model as model_from_cadnano_json
 
 """ vHelix """
 from .polygon_mesh import parse_maya_file, convert_maya_to_segments
+from ..model.dna_sequence import m13 as m13seq
 
 """ Atomic PDB """
 from .segmentmodel_from_pdb import SegmentModelFromPdb
@@ -19,7 +20,9 @@ def read_cadnano(json_file, **model_parameters):
 def read_vhelix(maya_file, **model_parameters):
     data = parse_maya_file(maya_file)
     segments, dsSegmentDict = convert_maya_to_segments( data )
-    return SegmentModel( segments,**model_parameters )
+    model = SegmentModel( segments,**model_parameters )
+    model.set_sequence(m13seq*10)
+    return model
 
 def read_atomic_pdb(pdb_file, **model_parameters):
     return SegmentModelFromPdb(pdb_file)

dnarbd/readers/cadnano_segments.py

@@ -541,16 +541,9 @@ def read_model(json_data, sequence=None):
 
     if sequence is None or len(sequence) == 0:
         ## default m13mp18
-        sequence = list(m13seq)
-        try:
-            model.strands[0].set_sequence(sequence)
-        except:
-            ...
+        model.set_sequence(m13seq,force=False)
     else:
-        model.strands[0].set_sequence(sequence)
-
-    for s in model.segments:
-        s.randomize_unset_sequence()
+        model.set_sequence(sequence)
 
     return model