allpy: afed1fd8920c allpy/dna.py

allpy

view allpy/dna.py @ 1091:afed1fd8920c

Added backreferences to `Seqeunce`s from `Monomer`s (closes #49) WARNING! Please note that `Sequence` API almost changed entirely! WARNING! This commit immediately obsoletes classmethods `Monomer.from_code*`, `Monomer.from_name` and `Sequence.from_monomers`. Turns out, python can not pickle sets/dicts which have keys, which inderecly reference the set/dict itself: http://bugs.python.org/issue9269 -- which is excatly what we have in abundance after this change. To allow pickling added `__getstate__` to `Monomer` to return all attributes, except `sequence` and `__setstate__` to `Sequence`, which runs through all monomers and returns the `sequence` attribute back to where it belongs. WARNING! This MAY result in unexpected behaviour in some cases. (Which should be rare enough).

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Sat, 02 Jun 2012 19:33:42 +0400
parents	4a9b4503a027
children	c4c772e3ce86

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

24 result = self.types.Sequence(

25 name=self.name +"'",

26 description=self.description,

27 source=self.source

28 )

29 for monomer in reversed(self):

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

31 return result

33 class Column(base.Column):

34 types = dna

36 class Alignment(base.Alignment):

37 types = dna

39 class Block(Alignment, base.Block):

40 pass

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