update distance between module

src/bayes_to_seqpy.py

@@ -400,7 +400,9 @@ def seq_to_struct(
         if component<len(position_subsets)-1:
             dis = component_distance[component]
             if dis[1]<4:
-                dis[1]=4
+                dis[1]=10
+            else:
+                dis[1]=1.5*dis[1]
         if len(re_call) > 0:
             re_call = re_call + r")([ACGU]{"+str(2)+","+str(dis[1])+"})"
         if len(i) == 1:

src/validation.py

@@ -273,21 +273,23 @@ def cross_validation(modules_to_test):
                         print(scores[k])
                         crossval_results[i].append(scores[k])
                 else:
+                    continue
+                    found = False
                     new_seq,new_ss = [],[]
                     offset = 0
-                    if last-first<300:
+                    if last-first<400:
                         helices = BayesPairing.find_loops(ss)[1]
                         print("HELICES")
                         print(helices)
                         for helix in helices:
                             if first>helix[0] and last<helix[1]:
+                                found = True
                                 new_seq = seq[helix[0]:helix[1]] 
                                 new_ss = ss[helix[0]:helix[1]]
                                 offset = helix[0]
                                 break
-                            else:
-                                continue
-                        if len(new_seq)>400:
+                    
+                        if len(new_seq)>400 or found==False:
                             continue
                         #filler = 200-(last-first)
                         #split = random.randrange(0,filler)
@@ -308,9 +310,9 @@ def cross_validation(modules_to_test):
                             crossval_results[i].append(scores[k])
    
                         
-        cv_fn = "crossval_"+str(i)
+        cv_fn = "car_crossval_"+str(i)+".cPickle"
         pickle.dump(crossval_results[i],open(cv_fn,"wb"))
-    pickle.dump(crossval_results, open("crossval_results.cPickle","wb"))
+    pickle.dump(crossval_results, open("just_short_carnaval_crossval_results_fixed_max_len.cPickle","wb"))
 if __name__ == "__main__":
     modules_to_test = range(0,len(graphs))
     cross_validation(modules_to_test)