Method: Bio::NucleicAcid::Data#to_re

Defined in:

lib/bio/data/na.rb

#to_re(seq, rna = false) ⇒ Object

# File 'lib/bio/data/na.rb', line 160

def to_re(seq, rna = false)
  replace = {
    'y' => '[tcy]',
    'r' => '[agr]',
    'w' => '[atw]',
    's' => '[gcw]',
    '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