From fa55ef624843e33f33ba779a69f57438ecabb4b6 Mon Sep 17 00:00:00 2001 From: Suman Neupane Date: Tue, 9 May 2017 15:53:34 -0400 Subject: [PATCH] fixed error --- brnlenMCMC.py | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/brnlenMCMC.py b/brnlenMCMC.py index 4435021..2034c52 100644 --- a/brnlenMCMC.py +++ b/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 @@ def calcExpectedHeight(num_species, mu_over_s): rates_list = gammaRates(alpha) postorder = readnewick(treenewick()) result = prepareTree(postorder, readSeq.patterns(), rates_list) -# try1 = readSeq.patterns() result2 = mcmcbrn(postorder, readSeq.patterns(), rates_list)