1 """Code to transcribe DNA into RNA or back (DEPRECATED).
2
3 You are now encouraged to use the Seq object methods or the functions
4 in Bio.Seq instead.
5
6 This module is now deprecated, and will be removed in a future release of
7 Biopython.
8 """
9 import warnings
10 import Bio
11 warnings.warn("Bio.Translate and Bio.Transcribe are deprecated, and will be "\
12 "removed in a future release of Biopython. Please use the "\
13 "functions or object methods defined in Bio.Seq instead "\
14 "(described in the tutorial). If you want to continue to use "\
15 "this code, please get in contact with the Biopython developers "\
16 "via the mailing lists to avoid its permanent removal from "
17 +"Biopython.", \
18 Bio.BiopythonDeprecationWarning)
19
20
21 from Bio import Alphabet, Seq
22 from Bio.Alphabet import IUPAC
23
25 - def __init__(self, dna_alphabet, rna_alphabet):
28
35 assert rna.alphabet == self.rna_alphabet, \
36 "back transcribe has the wrong RNA alphabet"
37 s = rna.data
38 return Seq.Seq(s.replace("U", "T"), self.dna_alphabet)
39
40 generic_transcriber = Transcribe(Alphabet.generic_dna,
41 Alphabet.generic_rna)
42 ambiguous_transcriber = Transcribe(IUPAC.ambiguous_dna,
43 IUPAC.ambiguous_rna)
44 unambiguous_transcriber = Transcribe(IUPAC.unambiguous_dna,
45 IUPAC.unambiguous_rna)
46