allpy: allpy/dna.py annotate

allpy

Added class Column to different dna/rna/protein modules too

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Mon, 21 Nov 2011 18:40:16 +0300
parents	5f9e9c4e9ed6
children	08d892230e8c afed1fd8920c

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@930	18 def reverse_complemented(self):
dendik@930	19 """Return a new sequence, reverse-complement to self.
dendik@930	20
dendik@930	21 Name of the sequence is name of self with apostrophe added.
dendik@930	22 """
dendik@930	23 from_monomers = self.types.Sequence.from_monomers
dendik@930	24 from_code1 = self.types.Monomer.from_code1
dendik@930	25 complement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
dendik@930	26 complemented_monomers = [
dendik@930	27 from_code1(complement.get(monomer.code1, 'N'))
dendik@930	28 for monomer in self
dendik@930	29 ]
dendik@930	30 return from_monomers(
dendik@930	31 reversed(complemented_monomers),
dendik@930	32 self.name + "'",
dendik@930	33 self.description,
dendik@930	34 self.source
dendik@930	35 )
dendik@930	36
dendik@931	37 class Column(base.Column):
dendik@931	38 types = dna
dendik@931	39
dendik@382	40 class Alignment(base.Alignment):
dendik@382	41 types = dna
bnagaev@240	42
me@341	43 class Block(Alignment, base.Block):
me@341	44 pass
me@341	45
me@280	46 # vim: set ts=4 sts=4 sw=4 et: