allpy: 349316a4e941 allpy/dna.py

allpy

view allpy/dna.py @ 1112:349316a4e941

utils/markup_to_file: added ability to specify multiple markup file names for batch tranformation as positional arguments

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Fri, 29 Jun 2012 19:34:21 +0400
parents	afed1fd8920c
children

line source

1 import base

2 import data.codes

3 from data.genetic_code import standard_dna_code

5 import dna

6 import protein

8 class Monomer(base.Monomer):

9 """DNA monomers: nucleotides."""

10 type = 'dna'

11 types = dna

12 by_code1 = {}

13 by_code3 = {}

14 by_name = {}

15 Monomer._initialize(data.codes.dna)

17 class Sequence(base.Sequence):

18 types = dna

20 def reverse_complemented(self):

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

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

24 """

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

26 result = self.types.Sequence(

27 name=self.name +"'",

28 description=self.description,

29 source=self.source

30 )

31 for monomer in reversed(self):

32 result.append_monomer(complement.get(monomer.code1, 'N'))

33 return result

35 def translated(self, code=None, name=None, description=None, source=None):

36 """Return a new protein sequence translated from self.

38 `code` is a dict of triplet of dna `code1`s -> aminoacid `name`.

40 If `code` is not specified, the standard genetic code is used.

42 If `code` is specified, it may contain only the changed codons.

44 Class of proteins to use is `self.types.protein.Sequence`, you

45 are free to replace it at will.

47 Return new protein sequence where:

49 * `name` is self.name with "_tr" appended

50 * `description` is self.description with " translated" appended

51 * `source` is the same as self.source

52 """

53 if code:

54 code, modification = dict(standard_dna_code), code

55 code.update(modification)

56 else:

57 code = standard_dna_code

58 result = self.types.protein.Sequence([],

59 name=name or self.name + "_tr",

60 description=description or self.description + " translated",

61 source=source or self.source

62 )

63 seen_stop = False

64 for a, b, c in zip(self[::3], self[1::3], self[2::3]):

65 assert not seen_stop, "Stop-codon must be the last one"

66 triplet = a.code1 + b.code1 + c.code1

67 aa_name = code[triplet]

68 if aa_name == "Stop":

69 seen_stop = True

70 continue

71 result.append_monomer(name=aa_name)

72 return result

74 class Column(base.Column):

75 types = dna

77 class Alignment(base.Alignment):

78 types = dna

80 class Block(Alignment, base.Block):

81 pass

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