allpy: ee2c10aa74b8 allpy/dna.py

allpy

view allpy/dna.py @ 610:ee2c10aa74b8

paired_cores/score.py: change method of score evaluation Boundary positions of blocks are not considered. Columns represented with one sequence or pure gap columns are not considered. Calculate weighted average of number of connected components in columns. Weight of column = l / sum(l) (l = number of sequnces representing column)

author	boris (kodomo) <bnagaev@gmail.com>
date	Tue, 05 Apr 2011 23:11:41 +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: