allpy
annotate 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 |
| rev | line source |
|---|---|
| bnagaev@240 | 1 import base |
| me@353 | 2 import data.codes |
| me@280 | 3 |
| dendik@382 | 4 import dna |
| dendik@382 | 5 |
| me@328 | 6 class Monomer(base.Monomer): |
| me@328 | 7 """DNA monomers: nucleotides.""" |
| me@328 | 8 type = 'dna' |
| dendik@382 | 9 types = dna |
| me@280 | 10 by_code1 = {} |
| me@280 | 11 by_code3 = {} |
| me@280 | 12 by_name = {} |
| me@353 | 13 Monomer._initialize(data.codes.dna) |
| bnagaev@240 | 14 |
| bnagaev@240 | 15 class Sequence(base.Sequence): |
| dendik@382 | 16 types = dna |
| dendik@382 | 17 |
| dendik@382 | 18 class Alignment(base.Alignment): |
| dendik@382 | 19 types = dna |
| bnagaev@240 | 20 |
| me@341 | 21 class Block(Alignment, base.Block): |
| me@341 | 22 pass |
| me@341 | 23 |
| me@280 | 24 # vim: set ts=4 sts=4 sw=4 et: |