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Transcribe.py

00001 """Code to transcribe DNA into RNA or back (OBSOLETE).

You are now encouraged to use the Seq object methods or the functions
in Bio.Seq instead.

This module is now considered to be obsolete, and is likely to be deprecated
in a future release of Biopython, and later removed.
"""
import string

from Bio import Alphabet, Seq
from Bio.Alphabet import IUPAC

class Transcribe:
    def __init__(self, dna_alphabet, rna_alphabet):
        self.dna_alphabet = dna_alphabet
        self.rna_alphabet = rna_alphabet
        
    def transcribe(self, dna):
        assert dna.alphabet == self.dna_alphabet, \
               "transcribe has the wrong DNA alphabet"
        s = dna.data
        return Seq.Seq(string.replace(s, "T", "U"), self.rna_alphabet)
    def back_transcribe(self, rna):
        assert rna.alphabet == self.rna_alphabet, \
               "back transcribe has the wrong RNA alphabet"
        s = rna.data
        return Seq.Seq(string.replace(s, "U", "T"), self.dna_alphabet)

generic_transcriber = Transcribe(Alphabet.generic_dna,
                                 Alphabet.generic_rna)
ambiguous_transcriber = Transcribe(IUPAC.ambiguous_dna,
                                   IUPAC.ambiguous_rna)
unambiguous_transcriber = Transcribe(IUPAC.unambiguous_dna,
                                     IUPAC.unambiguous_rna)

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