allpy: allpy/dna.py annotate

allpy

Removed tests for long-removed "ss" markup

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Sat, 02 Jun 2012 21:56:13 +0400
parents	4a9b4503a027
children	c4c772e3ce86

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 complement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
dendik@1091	24 result = self.types.Sequence(
dendik@1091	25 name=self.name +"'",
dendik@1091	26 description=self.description,
dendik@1091	27 source=self.source
dendik@930	28 )
dendik@1091	29 for monomer in reversed(self):
dendik@1091	30 result.append_monomer(complement.get(monomer.code1, 'N'))
dendik@1091	31 return result
dendik@930	32
dendik@931	33 class Column(base.Column):
dendik@931	34 types = dna
dendik@931	35
dendik@382	36 class Alignment(base.Alignment):
dendik@382	37 types = dna
bnagaev@240	38
me@341	39 class Block(Alignment, base.Block):
me@341	40 pass
me@341	41
me@280	42 # vim: set ts=4 sts=4 sw=4 et: