allpy
annotate allpy/rna.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 | 6e87dcc73d8b |
| rev | line source |
|---|---|
| bnagaev@240 | 1 import base |
| me@353 | 2 import data.codes |
| me@281 | 3 |
| dendik@382 | 4 import rna |
| dendik@382 | 5 |
| me@328 | 6 class Monomer(base.Monomer): |
| me@328 | 7 """RNA monomers: nucleotides.""" |
| me@328 | 8 type = 'rna' |
| dendik@382 | 9 types = rna |
| me@281 | 10 by_code1 = {} |
| me@281 | 11 by_code3 = {} |
| me@281 | 12 by_name = {} |
| me@353 | 13 Monomer._initialize(data.codes.rna) |
| bnagaev@240 | 14 |
| bnagaev@240 | 15 class Sequence(base.Sequence): |
| dendik@382 | 16 types = rna |
| bnagaev@240 | 17 |
| me@341 | 18 class Block(Alignment, base.Block): |
| me@341 | 19 pass |
| me@341 | 20 |
| dendik@379 | 21 class Alignment(base.Alignment): |
| dendik@382 | 22 types = rna |
| dendik@379 | 23 |
| me@281 | 24 # vim: set ts=4 sts=4 sw=4 et: |