tree.py 文件源码

def add_translations(self):
        '''
        translate the nucleotide sequence into the proteins specified
        in self.proteins. these are expected to be SeqFeatures
        '''
        from Bio import Seq

        # Sort proteins by start position of the corresponding SeqFeature entry.
        sorted_proteins = sorted(self.proteins.items(), key=lambda protein_pair: protein_pair[1].start)

        for node in self.tree.find_clades(order='preorder'):
            if not hasattr(node, "translations"):
                # Maintain genomic order of protein translations for easy
                # assembly by downstream functions.
                node.translations=OrderedDict()
                node.aa_mutations = {}

            for prot, feature in sorted_proteins:
                node.translations[prot] = Seq.translate(str(feature.extract(Seq.Seq("".join(node.sequence)))).replace('-', 'N'))

                if node.up is None:
                    node.aa_mutations[prot] = []
                else:
                    node.aa_mutations[prot] = [(a,pos,d) for pos, (a,d) in
                                               enumerate(zip(node.up.translations[prot],
                                                             node.translations[prot])) if a!=d]

        self.dump_attr.append('translations')