process.py 文件源码

def clock_filter(self):
        if self.config["clock_filter"] == False:
            return
        self.tree.tt.clock_filter(reroot='best', n_iqd=self.config["clock_filter"]["n_iqd"], plot=self.config["clock_filter"]["plot"])

        leaves = [x for x in self.tree.tree.get_terminals()]
        for n in leaves:
            if n.bad_branch:
                self.tree.tt.tree.prune(n)
                print('pruning leaf ', n.name)
        if self.config["clock_filter"]["remove_deep_splits"]:
            self.tree.tt.tree.ladderize()
            current_root = self.tree.tt.tree.root
            if sum([x.branch_length for x in current_root])>0.1 \
                and sum([x.count_terminals() for x in current_root.clades[:-1]])<5:
                new_root = current_root.clades[-1]
                new_root.up=False
                self.tree.tt.tree.root = new_root
                with open(self.output_path+"_outliers.txt", 'a') as ofile:
                    for x in current_root.clades[:-1]:
                        ofile.write("\n".join([leaf.name for leaf in x.get_terminals()])+'\n')

        self.tree.tt.prepare_tree()