sequences_process.py 文件源码

def translate(self):
        '''
        make alignments of translations.
        '''
        from Bio.Seq import CodonTable
        codon_table  = CodonTable.ambiguous_dna_by_name['Standard'].forward_table
        self.translations={}
        if not hasattr(self, "proteins"): # ensure dictionary to hold annotation
            self.proteins={}

        # add a default translation of the entire sequence unless otherwise specified
        if len(self.proteins)==0:
            self.proteins.update({'cds':FeatureLocation(start=0,
                end=self.aln.get_alignment_length(), strand=1)})

        # loop over all proteins and create one MSA for each
        for prot in self.proteins:
            aa_seqs = []
            for seq in self.aln:
                tmpseq = self.proteins[prot].extract(seq)
                translated_seq, translation_exception = safe_translate(str(tmpseq.seq), report_exceptions=True)
                if translation_exception:
                    self.log.notify("Trouble translating because of invalid codons %s" % seq.id)

                tmpseq.seq = Seq(translated_seq)

                # copy attributes
                tmpseq.attributes = seq.attributes
                aa_seqs.append(tmpseq)
            self.translations[prot] = MultipleSeqAlignment(aa_seqs)