Fixes a bug which was making some clustering going into an infinite loop when doing successor checking.

Author: nadiadavidson

BuildSuperTranscript.py

@@ -24,10 +24,11 @@ def successor_check(graph,n,tmerge):
     ess = [node for node in graph.successors(n)] #Get list of succesors
     #Succesor node only has one incoming path and is the only option for the previous node
     #Run until there is no successor node to add 
-    while(len(ess)==1 and len(graph.in_edges(ess))<=1):
+    #check if ess is already in tmerge list (for case of a looped chain)
+    while(len(ess)==1 and len(graph.in_edges(ess))<=1 and (ess[0] not in tmerge)):
         tmerge.append(ess[0])
         ess = [node for node in graph.successors(ess[0])]
-        #might need to check if ess is already in tmerge list (for case of a looped chain)????
+
     #return the list of nodes to merge
     return(tmerge)
 

Lace.py

@@ -184,8 +184,8 @@ def Split(genome,corsetfile,ncore,maxTran,outdir,full_clean):
     print("(  )    / _\  /    )(  __)")
     print("/  (_/\/    \(  (__  ) _) ")
     print("\_____/\_/\_/\_____)(____)")
-    print("Lace Version: 1.12")
-    print("Last Editted: 22/02/19")
+    print("Lace Version: 1.13")
+    print("Last Editted: 10/03/19")
 
 
     #Make argument parser