allpy: 3cc7ef543da5 allpy/dna.py

allpy

view allpy/dna.py @ 1049:3cc7ef543da5

allpy: do not print debugging messages, unless allpy.config.debug Note: new config variable was introduced: allpy.config.debug. By default, allpy.config.debug=False This is draft commit, since this feature was not properly discussed see 152

author	Boris Nagaev <bnagaev@gmail.com>
date	Sun, 25 Mar 2012 22:54:35 +0400
parents	5f9e9c4e9ed6
children	08d892230e8c afed1fd8920c

line source

1 import base

2 import data.codes

4 import dna

6 class Monomer(base.Monomer):

7 """DNA monomers: nucleotides."""

8 type = 'dna'

9 types = dna

10 by_code1 = {}

11 by_code3 = {}

12 by_name = {}

13 Monomer._initialize(data.codes.dna)

15 class Sequence(base.Sequence):

16 types = dna

18 def reverse_complemented(self):

19 """Return a new sequence, reverse-complement to self.

21 Name of the sequence is name of self with apostrophe added.

22 """

23 from_monomers = self.types.Sequence.from_monomers

24 from_code1 = self.types.Monomer.from_code1

25 complement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}

26 complemented_monomers = [

27 from_code1(complement.get(monomer.code1, 'N'))

28 for monomer in self

29 ]

30 return from_monomers(

31 reversed(complemented_monomers),

32 self.name + "'",

33 self.description,

34 self.source

35 )

37 class Column(base.Column):

38 types = dna

40 class Alignment(base.Alignment):

41 types = dna

43 class Block(Alignment, base.Block):

44 pass

46 # vim: set ts=4 sts=4 sw=4 et: