Class: Bio::DB::Primer3::Primer3Record

Inherits:
Object
  • Object
show all
Includes:
Comparable
Defined in:
lib/bio/db/primer3.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Primer3Record

Returns a new instance of Primer3Record.



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# File 'lib/bio/db/primer3.rb', line 438

def initialize
  @properties = Hash.new
  @scores = Hash.new
  @scores[:chromosome_specific] = 1000
  @scores[:chromosome_semispecific] = 100
  @scores[:chromosome_nonspecific] = 0
  @scores[:exon] = 50

end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(method_name, *args) ⇒ Object

Raises:

  • (NoMethodError) 


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# File 'lib/bio/db/primer3.rb', line 326

def method_missing(method_name, *args)
  return @properties[method_name] if @properties[method_name] 
  $stderr.puts "Missing #{method_name}"
  $stderr.puts @properties.inspect
  raise NoMethodError.new() 
end

Instance Attribute Details

#polymorphism ⇒ Object

Returns the value of attribute polymorphism.



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# File 'lib/bio/db/primer3.rb', line 306

def polymorphism
  @polymorphism
end

#properties ⇒ Object

Returns the value of attribute properties.



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# File 'lib/bio/db/primer3.rb', line 306

def properties
  @properties
end

#socres ⇒ Object

Returns the value of attribute socres.



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# File 'lib/bio/db/primer3.rb', line 307

def socres
  @socres
end

Class Method Details

.parse_file(filename) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 523

def self.parse_file(filename)
  File.open(filename) do | f |
    record = Primer3Record.new
    f.each_line do | line |
      line.chomp!
      if line == "="

        record.parse_blocks
        yield record
        record = Primer3Record.new
      else
        tokens = line.split("=")
        i = 0
        reg = ""
        #TODO: Look if there is a join function or something similar to go around this... 
        tokens.each do |tok|
          if i > 0
            if i > 1
              reg << "="
            end
            reg << tok
          end
          i+=1
        end
        record.properties[tokens[0].downcase.to_sym] = reg
      end
    end
  end
end

Instance Method Details

#<=>(anOther) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 354

def <=>(anOther)
  return  anOther.score <=> score
end

#best_pair ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 310

def best_pair
  return @best_pair if @best_pair
  @best_pair = nil
  @primerPairs.each do | primer |
    @best_pair = primer if @best_pair == nil
    @best_pair = primer if primer.size < @best_pair.size
  end
  #@best_pair = @primerPairs.min
  @best_pair
end

#chromosome ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 480

def chromosome
  return @chromosome if @parsed
  parse_header
  @chromosome
end

#exon? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/db/primer3.rb', line 498

def exon?
  return @exon if @parsed
  parse_header
  @exon
end

#find_left_tm(primer) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 333

def find_left_tm(primer)
  last = size - 1
  (0..last).each do | i |
    seq_prop = "primer_left_#{i}_sequence".to_sym
    #        $stderr.puts seq_prop
    temp_property = "primer_left_#{i}_tm".to_sym  
    #       $stderr.puts "comparing  #{@properties[seq_prop] } == #{primer}"
    return @properties[temp_property]  if @properties[seq_prop] == primer

  end
  return nil
end

#homeologous? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/db/primer3.rb', line 486

def homeologous?
  return @homeologous if @parsed
  parse_header
  @homeologous
end

#left_coordinates ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 366

def left_coordinates
  #@left_coordinates = parse_coordinates(self.primer_left_0) unless @left_coordinates 
  @left_coordinates = best_pair.left.coordinates
  @left_coordinates 
end

#left_primer ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 380

def left_primer
  #@left_primer = self.sequence_template[left_coordinates[0],left_coordinates[1]] unless @left_primer
  @left_primer = best_pair.left.sequence
  @left_primer
end

#left_primer_snp(snp) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 386

def left_primer_snp(snp)
  tmp_primer = String.new(left_primer)
  if self.orientation == :forward
    base_original = snp.original 
    base_snp = snp.snp
  elsif self.orientation == :reverse
    base_original = reverse_complement_string(snp.original )
    base_snp = reverse_complement_string(snp.snp)
  else
    raise Primer3Exception.new "#{self.orientation} is not a valid orientation"
  end

  # puts "#{snp.to_s} #{self.orientation} #{tmp_primer[-1] } #{base_original} #{base_snp}"
  if tmp_primer[-1] == base_original
    tmp_primer[-1] = base_snp
  elsif tmp_primer[-1] == base_snp
    tmp_primer[-1] = base_original  
  else
    raise Primer3Exception.new "#{tmp_primer} doesnt end in a base in the SNP #{snp.to_s}"
  end
  #puts "tmp_primer: #{tmp_primer}"
  return tmp_primer
end

#left_primer_with_coordinates(coordinates, other_orientation) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 410

def left_primer_with_coordinates(coordinates, other_orientation)

  seq = self.sequence_template
  #puts "Left coordinates: #{seq}"
  seq = reverse_complement_string(seq) if self.orientation != other_orientation

  seq[coordinates[0],coordinates[1]] 
end

#line ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 504

def line
  return @line if @parsed
  parse_header
  @line
end

#orientation ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 474

def orientation
  return @orientation if @parsed
  parse_header
  @orientation
end

#parse_blocks ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 514

def parse_blocks
  total_blocks = size - 1 
  @primerPairs = Array.new
  for i in 0..total_blocks
    @primerPairs << PrimerPair.new(self, i)
  end

end

#parse_coordinates(str) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 358

def parse_coordinates(str)
  coords = str.split(',')
  coords[0] = coords[0].to_i
  coords[1] = coords[1].to_i
  coords
end

#parse_header ⇒ Object

CL3339Contig1:T509C AvocetS chromosome_specific exon 4D forward



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# File 'lib/bio/db/primer3.rb', line 455

def parse_header
  #puts "Parsing header: '#{self.sequence_id}'"
  @snp, @line, @type, @in, @polymorphism, @chromosome, @orientation   = self.sequence_id.split(" ")  
  @type = @type.to_sym
  if @in
    @in = @in.to_sym == :exon 
  else
    @exon = false
  end

  if @polymorphism.to_sym == :homeologous
    @homeologous = true
  else
    @homeologous = false
  end
  @parsed = true
  @orientation = @orientation.to_sym
end

#primer_error ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 321

def primer_error
  return @properties[:primer_error] if @properties[:primer_error]
  return nil
end

#product_length ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 434

def product_length
  return best_pair.size
end

#reverse_complement_string(sequenc_str) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 419

def reverse_complement_string(sequenc_str)
  complement = sequenc_str.tr('atgcrymkdhvbswnATGCRYMKDHVBSWN', 'tacgyrkmhdbvswnTACGYRKMHDBVSWN')
  complement.reverse!
end

#right_coordinates ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 372

def right_coordinates
  unless @right_coordinates 
    @right_coordinates = best_pair.right.coordinates
    @right_coordinates[0] = @right_coordinates[0] - @right_coordinates[1] + 1
  end
  @right_coordinates 
end

#right_primer ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 430

def right_primer
  return best_pair.right.sequence
end

#right_primer_delete ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 424

def right_primer_delete
  @right_primer = self.sequence_template[right_coordinates[0],right_coordinates[1]] unless @right_primer
  @right_primer = reverse_complement_string(@right_primer)
  @right_primer
end

#score ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 346

def score
  ret = 0
  ret += @scores[type]
  ret += @scores[:exon] if exon?
  ret -= product_length
  ret
end

#size ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 510

def size
  @properties[:primer_pair_num_returned].to_i
end

#snp ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 448

def snp
  return @snp if @snp
  parse_header
  @snp
end

#type ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 492

def type
  return @type if @parsed
  parse_header
  @type
end