allpy: 69079d72d207 allpy/dna.py

allpy

view allpy/dna.py @ 640:69079d72d207

allpy.fileio: use stdin/stdout when communicating with EMBOSS [closes #38] The new implementation allows using any special files for fileio, including stdin/stdout, urllib, StringIO, etc. The new implementation is also cleaner and not prone to leaving temporary files behind in any cases.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Fri, 03 Jun 2011 15:29:47 +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: