Added test to check that model_from_basepair_stack_3prime works with circular...

Added test to check that model_from_basepair_stack_3prime works with circular ssDNA; removed warnings and made function work with lists instead of numpy arrays

mrdna/readers/segmentmodel_from_lists.py

@@ -39,7 +39,7 @@ def _primes_list_to_strands(three_prime, five_prime):
         strand_is_circular.append(False)
 
     while True:
-        print("WARNING: working on circular strand {}".format(len(strands)))
+        ## print("WARNING: working on circular strand {}".format(len(strands)))
         ids = np.where(idx_to_strand < 0)[0]
         if len(ids) == 0: break
         build_strand(ids[0],
@@ -232,6 +232,8 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
         basepair,three_prime = [np.array(a,dtype=np.int) for a in inputs]
     except:
         raise TypeError("One or more of the input lists could not be converted into a numpy array")
+    inputs = (basepair,three_prime)
+    coordinate = np.array(coordinate)
 
     if np.any( [len(a.shape) > 1 for a in inputs] ):
         raise ValueError("One or more of the input lists has the wrong dimensionality")
@@ -248,6 +250,7 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
         raise ValueError("The 'sequence' parameter is the wrong length {} != {}".format(len(sequence),num_nt))
 
     if orientation is not None:
+        orientation = np.array(orientation)
         if len(orientation.shape) != 3:
             raise ValueError("The 'orientation' array has the wrong dimensionality (should be Nx3x3)")
         if orientation.shape != (num_nt,3,3):
@@ -291,8 +294,6 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
     for s,c in zip(strands, strand_is_circular):
         ss_residues = s[np.where(hmap[s] < 0)[0]]
         if len(ss_residues) == 0: continue
-        if c:
-            print("WARNING: Circular ssDNA strands may not be modeled correctly")
         resid_diff = np.diff(ss_residues)
         
         tmp = np.where( resid_diff != 1 )[0]
@@ -403,3 +404,20 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
             s.randomize_unset_sequence()
 
     return model
+
+def UNIT_circular():
+    """ Make a circular DNA strand, with dsDNA in the middle """
+    coordinate = [(0,0,3.4*i) for i in range(7)]
+    stack = -1*np.ones(len(coordinate))
+    three_prime = [ 1, 2, 4,-1, 6, 3, 0]
+    basepair    = [-1,-1, 3, 2, 5, 4,-1]
+    stack       = [-1,-1, 4,-1,-1, 3,-1]
+    for i in [3,5]:
+        coordinate[i] = (1,0,3.4*i)
+
+    model = model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
+                                             max_basepairs_per_bead=1,
+                                             max_nucleotides_per_bead=1,
+                                             local_twist=True)
+
+    model.simulate(output_name='circular', directory='unittest')