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 533

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 421

def method_missing(method_name, *args)
  return @properties[method_name] if @properties[method_name] 
  $stderr.puts "Missing #{method_name}"
  $stderr.puts @properties.inspect
  return "" #if a property is missing, return blank. 
  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 401

def polymorphism
  @polymorphism
end

#properties ⇒ Object

Returns the value of attribute properties.



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# File 'lib/bio/db/primer3.rb', line 401

def properties
  @properties
end

#scores ⇒ Object

Returns the value of attribute scores.



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# File 'lib/bio/db/primer3.rb', line 402

def scores
  @scores
end

Class Method Details

.parse_file(filename, scores: nil) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 629

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

        record.parse_blocks
        yield record
        record = Primer3Record.new
        record.scores = scores if scores
      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

.reverse_complement_string(sequenc_str) ⇒ Object 



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

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

Instance Method Details

#<=>(anOther) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 450

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

#best_pair ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 405

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 586

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 604

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 429

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

#homoeologous? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/db/primer3.rb', line 592

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

#left_coordinates ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 462

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 476

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 482

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
    #puts self.inspect
    base_original =Primer3Record.reverse_complement_string(snp.original )
    base_snp = Primer3Record.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 507

def left_primer_with_coordinates(coordinates, other_orientation)

  seq = self.sequence_template
  seq = Primer3Record.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 610

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

#orientation ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 580

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

#parse_blocks ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 620

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 454

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 550

def parse_header
  #puts "Parsing header: '#{self.sequence_id}'"
  arr = self.sequence_id.split(" ")

  #if arr.size == 7 This validation can be useful to get the best primers regardless of the chromosome, 
  #But it is commented as it will require further testing. 
  @snp, @line, @type, @in, @polymorphism, @chromosome, @orientation  = arr  
  #else 
  #  if arr.size == 6
  #    @snp, @line, @type, @in, @polymorphism, @orientation  = arr
  #    @chromosome = ""   
  #  end 
  #end

  @type = @type.to_sym
  if @in
    @in = @in.to_sym == :exon 
  else
    @exon = false
  end

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

#primer_error ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 416

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 529

def product_length
  return best_pair.size
end

#right_coordinates ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 468

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 525

def right_primer
  return best_pair.right.sequence
end

#right_primer_delete ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 519

def right_primer_delete
  @right_primer = self.sequence_template[right_coordinates[0],right_coordinates[1]] unless @right_primer
  @right_primer = Primer3Record.reverse_complement_string(@right_primer)
  @right_primer
end

#score ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 442

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 616

def size
  @properties[:primer_pair_num_returned].to_i
end

#snp ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 543

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

#type ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 598

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