def trainTree(conf, stree, gene2species): args = conf["REST"] treefiles = [] for arg in args: treefiles.extend(util.shellparser(arg)) util.tic("reading trees") trees = [] prog = progress.ProgressBar(len(treefiles)) for treefile in treefiles: prog.update() trees.append(treelib.read_tree(treefile)) # even out top two branches totlen = trees[-1].root.children[0].dist + \ trees[-1].root.children[1].dist trees[-1].root.children[0].dist = totlen / 2.0 trees[-1].root.children[1].dist = totlen / 2.0 util.toc() params = Spidir.learnModel(trees, stree, gene2species, conf["trainstats"], filenames=treefiles) Spidir.writeParams(conf["param"], params)