treeanc.py 文件源码

def get_reconstructed_alignment(self):
        """
        Get the multiple sequence alignment including reconstructed sequences for
        the internal nodes.
        """
        from Bio.Align import MultipleSeqAlignment
        from Bio.Seq import Seq
        from Bio.SeqRecord import SeqRecord
        self.logger("TreeAnc.get_reconstructed_alignment ...",2)
        if not hasattr(self.tree.root, 'sequence'):
            self.logger("TreeAnc.reconstructed_alignment... reconstruction not yet done",3)
            self.reconstruct_anc('ml')

        new_aln = MultipleSeqAlignment([SeqRecord(id=n.name, seq=Seq("".join(n.sequence)), description="")
                                        for n in self.tree.find_clades()])

        return new_aln