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)