Class: Microhomology::Talen

Inherits:
Object
  • Object
show all
Defined in:
lib/microhomology.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(key) ⇒ Talen

Returns a new instance of Talen.



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# File 'lib/microhomology.rb', line 78

def initialize(key)
  @key = key
  @dna = open(get_ensembl_url).read
  @results = perform_microhomology
end

Instance Attribute Details

#dna ⇒ Object

Returns the value of attribute dna.



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# File 'lib/microhomology.rb', line 76

def dna
  @dna
end

#key ⇒ Object

Returns the value of attribute key.



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# File 'lib/microhomology.rb', line 76

def key
  @key
end

#results ⇒ Object

Returns the value of attribute results.



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# File 'lib/microhomology.rb', line 76

def results
  @results
end

Instance Method Details

#exons ⇒ Object 



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# File 'lib/microhomology.rb', line 88

def exons
  self.dna.scan /[A-Z]+/
end

#get_ensembl_url ⇒ Object 



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# File 'lib/microhomology.rb', line 84

def get_ensembl_url
  "http://rest.ensembl.org/sequence/id/#{self.key}?content-type=text/plain;mask_feature=true"
end

#introns ⇒ Object 



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# File 'lib/microhomology.rb', line 92

def introns
  self.dna.scan /[a-z]+/
end

#perform_microhomology ⇒ Object 



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# File 'lib/microhomology.rb', line 96

def perform_microhomology
  targets = []
  self.dna.scan(Microhomology::TALEN) do |talen|
    targets << {
                "target" => talen,
                "first" => Regexp.last_match.offset(0).first, 
                "last" => Regexp.last_match.offset(0).last,
                "microhomology" => []
                }
  end

  if targets
    targets.each do |target|

      talen_site = Bio::Sequence::NA.new(target['target'])
      talen_site_complement = talen_site.complement.reverse

      talen1  = talen_site[0..15]
      spacer1 = talen_site[16..22]
      spacer2 = talen_site[23..30]
      talen2  = talen_site[31..47]

      talen_forward = Bio::Sequence::NA.new("#{talen1}#{spacer2}#{spacer1}#{talen2}")
      talen_reverse = talen_forward.complement.reverse

      target["microhomology"] << { 
          "forward_strand" => "#{talen_site.upcase}",
          "reverse_strand" => "#{talen_site_complement.upcase}",
          "oligo_forward" => "#{talen_forward.upcase}",
          "oligo_reverse" => "#{talen_reverse.upcase}"
        }
    end
    targets
  else
    "Sorry, no TALEN targets found."
  end
end