finished paper

bayespairing/src/bayes_to_seqpy.py

@@ -421,7 +421,7 @@ def adjust_aln(best_struct,positions,better_positions):
     return new_best_struct
 
 def preserve_rotation(position_subsets):
-    print(position_subsets)
+    #print(position_subsets)
     if len(position_subsets)<3:
         #print("not a junction")
         permutations = list(itertools.permutations(position_subsets))
@@ -647,6 +647,7 @@ def seq_to_struct(
             #used to do 0.4,0.6,0.8,1 for paper run
             for subseq in [0.4,0.6,0.8,1]:
                 this_seq = seq[0:int(len(seq) * subseq)]
+                #print("CURRENT REGEX:",res[index])
                 r =  regex.compile(res[index],flag=regex.BESTMATCH)
                 iters = r.finditer(str(this_seq), overlapped=True)
                 for a in iters: