allpy: 21cfc7897a8f allpy/protein.py

allpy

view allpy/protein.py @ 711:21cfc7897a8f

Implemented markup fileIO (closes #56) This is done by adding file format 'markup' or 'markup:formatname', where 'formatname' is otherwise known alignment format. The file format for is described briefly in fileio.MarkupFile docstrings. This commit also contains example of defining Markup saving mixin: markups.IntMarkupMixin and a test for it.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Thu, 07 Jul 2011 22:32:21 +0400
parents	387f692e2356
children	4a9b4503a027

line source

1 import base

2 import data.codes

4 import protein

6 class Monomer(base.Monomer):

7 """Protein monomers: aminoacids."""

8 type = 'protein'

9 types = protein

10 by_code1 = {}

11 by_code3 = {}

12 by_name = {}

13 Monomer._initialize(data.codes.protein)

15 class Protein(list):

16 """User defined protein; list of protein_sequences."""

17 pass

19 class Sequence(base.Sequence):

20 types = protein

22 class Alignment(base.Alignment):

23 types = protein

25 class Block(Alignment, base.Block):

26 pass

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