fixed error

brnlenMCMC.py

@@ -129,7 +129,7 @@ def allocatePartial(node, patterns, rates):
                 node.partial[i*16+l*4 + 1] = pfromC_lchild*pfromC_rchild
 
                 #######################################################
-# 
+
                 pGA = pdiff*(node.lchild.partial[i*16+l*4 + 0])
                 pGC = pdiff*(node.lchild.partial[i*16+l*4 + 1])
                 pGG = psame*(node.lchild.partial[i*16+l*4 + 2])
@@ -166,10 +166,6 @@ def allocatePartial(node, patterns, rates):
         log_like = sum(like_list)           
         return log_like
 
-def replaedglen():
-    old_newick = readnewick(tree)
-
-
 
 def mcmcbrn(postorder, patterns, rates):
     nodes = readnewick(treenewick())
@@ -199,7 +195,6 @@ def mcmcbrn(postorder, patterns, rates):
     print '**************************'
 
     newf.write('\n')
-#     print
     for r in range(n_gen):
         for i in range(len(postorder)):
             preedgelen = nodes[i].edgelen
@@ -246,7 +241,7 @@ def mcmcbrn(postorder, patterns, rates):
             print 
             print '**************************'
 
-            newf.flush()
+#             newf.flush()
 
         mcmc+=1
 
@@ -491,5 +486,4 @@ if __name__ == '__main__':
     rates_list = gammaRates(alpha)
     postorder = readnewick(treenewick())
     result =  prepareTree(postorder, readSeq.patterns(), rates_list)
-#     try1 = readSeq.patterns()
     result2 = mcmcbrn(postorder, readSeq.patterns(), rates_list)