allpy: 80043822a41e allpy/dna.py

allpy

view allpy/dna.py @ 704:80043822a41e

Added fileio.File.read_alignment and fileio.File.write_alignment [closes #57] This is now the recommended interface. In the following commits this interface will be used to write markup together with alignment. Previously, fileio received the alignment torn-apart into sequence representations as strings with gaps, sequence names and descriptions. Now, fileio tears the alignment apart by itself.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Thu, 07 Jul 2011 19:21:12 +0400
parents	5639138f619a
children	5f9e9c4e9ed6 e461a5529338

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 class Alignment(base.Alignment):

19 types = dna

21 class Block(Alignment, base.Block):

22 pass

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