for i in range(1,len(yeastset)):
tree = yeastset[i]
treefiles = [tree + "_bayes_treeout.txt",tree + "_raxml_treeout.txt",tree + "_BEAST_treeout.txt",tree + "_phyml_treeout.txt"]
for m in range(len(models)):
topo_data_file = topo_data_dir + "/yeast_" + models[m] + "_" + str(topoPicked) + "_topomatches.txt"
treehome = basedir + "/" + yeastset[i] + "/" + models[m] + "/"
infile = open(topo_data_file,'r')
sameTop = 1
for line in infile:
temp = line.split()
if (temp[0] == "'" + str(i) + "'"):
if (temp[1] == "TRUE"):
sameTop = 1
break
elif (temp[2] == "TRUE"):
sameTop = 2
break
logplot = LogMapPlotter(tree, treefiles[m], treehome, models[m], rooted=False)
logplot.split_topos()
logplot.make_centres(sameTop)
logplot.make_coords(sameTop)
#os.remove(tree + str(i) + "_" + models[m] + "_allcoords.r")
#os.remove(tree + str(i) + "_" + models[m] + "_allcoords_norm3D.r")
logplot.plot_coords_all()
logplot.plot_coords_quads()
# Next step: figure out edges for a 'progression' in topologies
if not os.path.exists(treehome + tree + str(i) + "_" + models[m] + "_norms.txt"):
ln = LeafNorm(tree + str(i), treefiles[m], treehome, models[m])
ln.makeNormFiles()
# 4. Coordinate discovery for logmaps
#models = ["bayes","raxml","phyml"]
#models = ["bayes"]
models = ["BEAST"]
for i in range(1,runNum):
for m in range(len(models)):
model_dir = "/" + models[m] + "/"
treehome = basedir + "/" + tree + str(i) + model_dir
#treefiles = [tree + str(i) + "_bayes_treeout.txt",tree + str(i) + "_raxml_treeout.txt",tree + str(i) + "_phyml_treeout.txt"]
treefiles = [tree + str(i) + "_BEAST_treeout.txt"]
#treefiles = [tree + str(i) + "_raxml_treeout.txt",tree + str(i) + "_BEAST_treeout.txt",tree + str(i) + "_phyml_treeout.txt"]
logplot = LogMapPlotter(tree + str(i), treefiles[m], treehome, models[m], rooted=True)
#logplot = LogMapPlotter(tree + str(i), treefiles[m], treehome, models[m], rooted=False)
logplot.split_topos()
logplot.make_centres()
logplot.make_coords()
#os.remove(tree + str(i) + "_" + models[m] + "_allcoords.r")
#os.remove(tree + str(i) + "_" + models[m] + "_allcoords_norm3D.r")
logplot.plot_coords_all()
#logplot.plot_coords_quads()
# To delete directories and their contents:
#shutil.rmtree(treehome + "quadrant_plots")
#orderByLogMap(tree + str(i), basedir + "/" + tree + str(i), models[m], best=False, orderby=1, bynorm=False)
#orderByLogMap(tree + str(i), basedir + "/" + tree + str(i), models[m], best=False, orderby=1, bynorm=True)
