feature.py 文件源码

def translation(self):
        """
        Returns the amino acid sequence of self
        B = "Asx";  Aspartic acid (R) or Asparagine (N)
        X = "Xxx";  Unknown or 'other' amino acid
        Z = "Glx";  Glutamic acid (E) or Glutamine (Q)
        J = "Xle";  Leucine (L) or Isoleucine (I), used in mass-spec (NMR)
        U = "Sec";  Selenocysteine
        O = "Pyl";  Pyrrolysine
        """
        codon_table = CodonTable.ambiguous_dna_by_id[self.transl_table]  
        seq = Seq(str(self.sequence()),IUPACAmbiguousDNA())
        translated_seq = seq.translate(codon_table).tostring().replace('B','X').replace('Z','X').replace('J','X')
        if '*' in translated_seq[:-1]: # check if premature stop codon in the translation
            logging.error('Stop codon found within the CDS. It will rise an error submiting the data to ENA. Please fix your gff file.')

        # remove the stop character. It's not accepted by embl
        if translated_seq[-1:] == "*":
            translated_seq = translated_seq[:-1]

        return translated_seq