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#
# bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
#
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License:: The Ruby License
#
module Bio
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
class RestrictionEnzyme
class DoubleStranded
# Align two SingleStrand objects and return a Result
# object with +primary+ and +complement+ accessors.
#
class AlignedStrands
extend CutSymbol
extend StringFormatting
# Creates a new object.
# ---
# *Returns*:: Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands object
def initialize; super; end
# The object returned for alignments
Result = Struct.new(:primary, :complement)
# Pad and align two String objects without cut symbols.
#
# This will look for the sub-sequence without left and right 'n' padding
# and re-apply 'n' padding to both strings on both sides equal to the
# maximum previous padding on that side.
#
# The sub-sequences stripped of left and right 'n' padding must be of equal
# length.
#
# Example:
# AlignedStrands.align('nngattacannnnn', 'nnnnnctaatgtnn') # =>
# <struct Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands::Result
# primary="nnnnngattacannnnn",
# complement="nnnnnctaatgtnnnnn">
#
# ---
# *Arguments*
# * +a+: Primary strand
# * +b+: Complementary strand
# *Returns*:: +Result+ object with equal padding on both strings
def self.align(a, b)
a = a.to_s
b = b.to_s
validate_input( strip_padding(a), strip_padding(b) )
left = [left_padding(a), left_padding(b)].sort.last
right = [right_padding(a), right_padding(b)].sort.last
p = left + strip_padding(a) + right
c = left + strip_padding(b) + right
Result.new(p,c)
end
# Pad and align two String objects with cut symbols.
#
# Example:
# AlignedStrands.with_cuts('nngattacannnnn', 'nnnnnctaatgtnn', [0, 10, 12], [0, 2, 12]) # =>
# <struct Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands::Result
# primary="n n n n^n g a t t a c a n n^n n^n",
# complement="n^n n^n n c t a a t g t n^n n n n">
#
# Notes:
# * To make room for the cut symbols each nucleotide is spaced out.
# * This is meant to be able to handle multiple cuts and completely
# unrelated cutsites on the two strands, therefore no biological
# algorithm assumptions (shortcuts) are made.
#
# The sequences stripped of left and right 'n' padding must be of equal
# length.
#
# ---
# *Arguments*
# * +a+: Primary sequence
# * +b+: Complementary sequence
# * +a_cuts+: Primary strand cut locations in 0-based index notation
# * +b_cuts+: Complementary strand cut locations in 0-based index notation
# *Returns*:: +Result+ object with equal padding on both strings and spacing between bases
def self.align_with_cuts(a,b,a_cuts,b_cuts)
a = a.to_s
b = b.to_s
validate_input( strip_padding(a), strip_padding(b) )
a_left, a_right = left_padding(a), right_padding(a)
b_left, b_right = left_padding(b), right_padding(b)
left_diff = a_left.length - b_left.length
right_diff = a_right.length - b_right.length
(right_diff > 0) ? (b_right += 'n' * right_diff) : (a_right += 'n' * right_diff.abs)
a_adjust = b_adjust = 0
if left_diff > 0
b_left += 'n' * left_diff
b_adjust = left_diff
else
a_left += 'n' * left_diff.abs
a_adjust = left_diff.abs
end
a = a_left + strip_padding(a) + a_right
b = b_left + strip_padding(b) + b_right
a_cuts.sort.reverse.each { |c| a.insert(c+1+a_adjust, cut_symbol) }
b_cuts.sort.reverse.each { |c| b.insert(c+1+b_adjust, cut_symbol) }
Result.new( add_spacing(a), add_spacing(b) )
end
#########
protected
#########
def self.validate_input(a,b)
unless a.size == b.size
err = "Result sequences are not the same size. Does not align sequences with differing lengths after strip_padding.\n"
err += "#{a.size}, #{a.inspect}\n"
err += "#{b.size}, #{b.inspect}"
raise ArgumentError, err
end
end
end # AlignedStrands
end # DoubleStranded
end # RestrictionEnzyme
end # Bio
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