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|
#
# = bio/data/na.rb - Nucleic Acids
#
# Copyright:: Copyright (C) 2001, 2005
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# == Synopsis
#
# Bio::NucleicAcid class contains data related to nucleic acids.
#
# == Usage
#
# Examples:
#
# require 'bio'
#
# puts "### na = Bio::NucleicAcid.new"
# na = Bio::NucleicAcid.new
#
# puts "# na.to_re('yrwskmbdhvnatgc')"
# p na.to_re('yrwskmbdhvnatgc')
#
# puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
# p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')
#
# puts "# na.weight('A')"
# p na.weight('A')
#
# puts "# Bio::NucleicAcid.weight('A')"
# p Bio::NucleicAcid.weight('A')
#
# puts "# na.weight('atgc')"
# p na.weight('atgc')
#
# puts "# Bio::NucleicAcid.weight('atgc')"
# p Bio::NucleicAcid.weight('atgc')
#
module Bio
class NucleicAcid
module Data
# IUPAC code
# * Faisst and Meyer (Nucleic Acids Res. 20:3-26, 1992)
# * http://www.ncbi.nlm.nih.gov/collab/FT/
NAMES = {
'y' => '[tc]',
'r' => '[ag]',
'w' => '[at]',
's' => '[gc]',
'k' => '[tg]',
'm' => '[ac]',
'b' => '[tgc]',
'd' => '[atg]',
'h' => '[atc]',
'v' => '[agc]',
'n' => '[atgc]',
'a' => 'a',
't' => 't',
'g' => 'g',
'c' => 'c',
'u' => 'u',
'A' => 'Adenine',
'T' => 'Thymine',
'G' => 'Guanine',
'C' => 'Cytosine',
'U' => 'Uracil',
'Y' => 'pYrimidine',
'R' => 'puRine',
'W' => 'Weak',
'S' => 'Strong',
'K' => 'Keto',
'M' => 'aroMatic',
'B' => 'not A',
'D' => 'not C',
'H' => 'not G',
'V' => 'not T',
}
WEIGHT = {
# Calculated by BioPerl's Bio::Tools::SeqStats.pm :-)
'a' => 135.15,
't' => 126.13,
'g' => 151.15,
'c' => 111.12,
'u' => 112.10,
:adenine => 135.15,
:thymine => 126.13,
:guanine => 151.15,
:cytosine => 111.12,
:uracil => 112.10,
:deoxyribose_phosphate => 196.11,
:ribose_phosphate => 212.11,
:hydrogen => 1.00794,
:water => 18.015,
}
def weight(x = nil, rna = nil)
if x
if x.length > 1
if rna
phosphate = WEIGHT[:ribose_phosphate]
else
phosphate = WEIGHT[:deoxyribose_phosphate]
end
hydrogen = WEIGHT[:hydrogen]
water = WEIGHT[:water]
total = 0.0
x.each_byte do |byte|
base = byte.chr.downcase
if WEIGHT[base]
total += WEIGHT[base] + phosphate - hydrogen * 2
else
raise "Error: invalid nucleic acid '#{base}'"
end
end
total -= water * (x.length - 1)
else
WEIGHT[x.to_s.downcase]
end
else
WEIGHT
end
end
def [](x)
NAMES[x]
end
# backward compatibility
def names
NAMES
end
alias na names
def name(x)
NAMES[x.to_s.upcase]
end
def to_re(seq, rna = false)
replace = {
'y' => '[tcy]',
'r' => '[agr]',
'w' => '[atw]',
's' => '[gcs]',
'k' => '[tgk]',
'm' => '[acm]',
'b' => '[tgcyskb]',
'd' => '[atgrwkd]',
'h' => '[atcwmyh]',
'v' => '[agcmrsv]',
'n' => '[atgcyrwskmbdhvn]'
}
replace.default = '.'
str = seq.to_s.downcase
str.gsub!(/[^atgcu]/) { |na|
replace[na]
}
if rna
str.tr!("t", "u")
end
Regexp.new(str)
end
end
# as instance methods
include Data
# as class methods
extend Data
end
end # module Bio
|
