Class: Bio::DB::Primer3::SNP

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

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ SNP

Returns a new instance of SNP.



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# File 'lib/bio/db/primer3.rb', line 67

def initialize
  @primers_line_1 = SortedSet.new
  @primers_line_2 = SortedSet.new
  @reguibs = SortedSet.new
end

Instance Attribute Details

#chromosome ⇒ Object

Returns the value of attribute chromosome.



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# File 'lib/bio/db/primer3.rb', line 55

def chromosome
  @chromosome
end

#gene ⇒ Object

Returns the value of attribute gene.



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# File 'lib/bio/db/primer3.rb', line 55

def gene
  @gene
end

#line_1 ⇒ Object

Returns the value of attribute line_1.



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# File 'lib/bio/db/primer3.rb', line 55

def line_1
  @line_1
end

#line_2 ⇒ Object

Returns the value of attribute line_2.



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# File 'lib/bio/db/primer3.rb', line 55

def line_2
  @line_2
end

#original ⇒ Object

Returns the value of attribute original.



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# File 'lib/bio/db/primer3.rb', line 55

def original
  @original
end

#position ⇒ Object

Returns the value of attribute position.



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# File 'lib/bio/db/primer3.rb', line 55

def position
  @position
end

#primer3_errors ⇒ Object

Returns the value of attribute primer3_errors.



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# File 'lib/bio/db/primer3.rb', line 61

def primer3_errors
  @primer3_errors
end

#primer3_line_1 ⇒ Object

Returns the value of attribute primer3_line_1.



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# File 'lib/bio/db/primer3.rb', line 56

def primer3_line_1
  @primer3_line_1
end

#primer3_line_2 ⇒ Object

Returns the value of attribute primer3_line_2.



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# File 'lib/bio/db/primer3.rb', line 56

def primer3_line_2
  @primer3_line_2
end

#primers_line_1 ⇒ Object

Returns the value of attribute primers_line_1.



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# File 'lib/bio/db/primer3.rb', line 57

def primers_line_1
  @primers_line_1
end

#primers_line_2 ⇒ Object

Returns the value of attribute primers_line_2.



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# File 'lib/bio/db/primer3.rb', line 57

def primers_line_2
  @primers_line_2
end

#regions ⇒ Object

Returns the value of attribute regions.



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# File 'lib/bio/db/primer3.rb', line 60

def regions
  @regions
end

#snp ⇒ Object

Returns the value of attribute snp.



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# File 'lib/bio/db/primer3.rb', line 55

def snp
  @snp
end

#snp_from ⇒ Object

Returns the value of attribute snp_from.



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# File 'lib/bio/db/primer3.rb', line 59

def snp_from
  @snp_from
end

#template_length ⇒ Object

Returns the value of attribute template_length.



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# File 'lib/bio/db/primer3.rb', line 56

def template_length
  @template_length
end

#used_contigs ⇒ Object

Returns the value of attribute used_contigs.



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# File 'lib/bio/db/primer3.rb', line 58

def used_contigs
  @used_contigs
end

Class Method Details

.parse(reg_str) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 248

def self.parse(reg_str)
  reg_str.chomp!
  snp = SNP.new
  snp.gene, snp.original, snp.position, snp.snp = reg_str.split(",")
  snp.position = snp.position.to_i
  snp.original.upcase!
  snp.snp.upcase!  
  snp
end

.parse_file(filename) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 258

def self.parse_file(filename)
  File.open(filename) do | f |
    f.each_line do | line |
      snp = SNP.parse(line)
      if snp.position > 0
        yield snp
      end
    end
  end
end

Instance Method Details

#add_record(primer3record) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 270

def add_record(primer3record)
  @primer3_errors = Array.new unless @primer3_errors
  @template_length = primer3record.sequence_template.size
   if primer3record.primer_error != nil 
      primer3_errors << primer3record
      return
    end
  case
  when primer3record.line == @line_1

    @line_1_template = primer3record.sequence_template

  when primer3record.line == @line_2
    @line_2_template = primer3record.sequence_template
  else
    raise Primer3Exception.new "#{primer3record.line} is not recognized (#{line_1}, #{line_2})"
  end

  if  primer3record.primer_left_num_returned.to_i > 0 
    case
    when primer3record.line == @line_1
      primers_line_1 << primer3record
      #puts primer3record.inspect
      @primer3_line_1 = primer3record if not @primer3_line_1  or @primer3_line_1 > primer3record
    when primer3record.line == @line_2
      primers_line_2 << primer3record
      @primer3_line_2 = primer3record if not @primer3_line_2 or @primer3_line_2 > primer3record
    else
      raise Primer3Exception.new "#{primer3record.line} is not recognized (#{line_1}, #{line_2})"
    end
  end
end

#find_left_primer_temp(primer) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 81

def find_left_primer_temp(primer)
  primers_line_1.each do |pr|
    return pr.find_left_tm(primer) if pr.find_left_tm(primer)
  end
  primers_line_2.each do |pr|
    return pr.find_left_tm(primer) if pr.find_left_tm(primer)
  end
  return "NA"
end

#find_primer_pair_first ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 92

def find_primer_pair_first
  primers_line_1.each do |pr|
    primer = pr.left_primer_snp(self)
    return pr if find_left_primer_temp(primer) != "NA"
  end
  nil
end

#find_primer_pair_second ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 100

def find_primer_pair_second
  primers_line_2.each do |pr|
    primer = pr.left_primer_snp(self)
    return pr if find_left_primer_temp(primer) != "NA"
  end
  nil
end

#line_1_name ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 63

def line_1_name
  "#{gene}:#{position}#{original}>#{snp} #{line_1}}"
end

#line_2_name ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 73

def line_2_name
  "#{gene}:#{position}#{original}>#{snp} #{line_2}}"
end

#print_primers ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 109

def print_primers
#TODO: Retrieve error messages
  left_start = 0
  left_end = 0
  right_start = 0
  right_end = 0
 #     exons = snp_from.exon_list.values
  
#      puts "Exons: #{exon_list.size}"
  
#      puts "It has the following exons: #{snp_in.exon_list.to_s}"
  values = Array.new
  #values << "#{gene},,#{template_length},"
  values << gene
  values << "#{original}#{position}#{snp}"
  values << template_length
  values << snp_from.chromosome
  values << regions.size
  values << regions.join("|")
  if primer3_line_1 and primer3_line_2
    values <<  primer3_line_1.polymorphism

    #Block that searches both if both pairs have a TM
    primer_2 = primer3_line_2.left_primer_with_coordinates(primer3_line_1.left_coordinates, primer3_line_1.orientation)
    primer_2_tm = find_left_primer_temp(primer_2)
    primer_1 = primer3_line_1.left_primer_with_coordinates(primer3_line_2.left_coordinates, primer3_line_2.orientation) 
    primer_1_tm = find_left_primer_temp(primer_1)
    #  $stderr.puts primer_1
    #  $stderr.puts primer_2
    if primer3_line_1 < primer3_line_2 and primer_2_tm != "NA"
      values << primer3_line_1.left_primer
      values << primer_2
      values << primer3_line_1.right_primer 
      values << primer3_line_1.type.to_s 
      values << primer3_line_1.orientation.to_s 
      values << primer3_line_1.best_pair.left.tm 
      values << primer_2_tm
      values << primer3_line_1.best_pair.right.tm
      values << "first" 
      values << primer3_line_1.best_pair.product_size
    elsif  primer_1_tm != "NA"
      values << primer_1
      values << primer3_line_2.left_primer
      values << primer3_line_2.right_primer
      values << primer3_line_2.type.to_s
      values << primer3_line_2.orientation.to_s
      values << primer_1_tm
      values << primer3_line_2.best_pair.left.tm
      values << primer3_line_2.best_pair.right.tm
      values << "second"
      values << primer3_line_2.best_pair.product_size
    else

      first_candidate = find_primer_pair_first
      second_candidate = find_primer_pair_second

      if first_candidate
        primer_2 = primer3_line_2.left_primer_with_coordinates(first_candidate.left_coordinates, first_candidate.orientation)
        primer_2_tm = find_left_primer_temp(primer_2)
      end
      if second_candidate
        #puts "input to search #{first_candidate.left_coordinates}"
        primer_1 = primer3_line_1.left_primer_with_coordinates(second_candidate.left_coordinates, second_candidate.orientation) 
        primer_1_tm = find_left_primer_temp(primer_1)
        #puts "In the other funky if #{primer_2}"
      end

      if first_candidate and second_candidate and first_candidate < second_candidate 
        #puts "A"
        values << first_candidate.left_primer
        values << primer_2
        values << first_candidate.right_primer 
        values << first_candidate.type.to_s 
        values << first_candidate.orientation.to_s 
        values << first_candidate.best_pair.left.tm 
        values << primer_2_tm
        values << first_candidate.best_pair.right.tm
        values << "first" 
        values << first_candidate.best_pair.product_size
      elsif  second_candidate 
        #puts "B"
        values << primer_1
        values << second_candidate.left_primer
        values << second_candidate.right_primer
        values << second_candidate.type.to_s
        values << second_candidate.orientation.to_s
        values << primer_1_tm
        values << second_candidate.best_pair.left.tm
        values << second_candidate.best_pair.right.tm
        values << "second"
        values << second_candidate.best_pair.product_size
      elsif  first_candidate 
        #puts "C"
        values << first_candidate.left_primer
        values << primer_2
        values << first_candidate.right_primer
        values << first_candidate.type.to_s
        values << first_candidate.orientation.to_s
        values << primer_2_tm
        values << first_candidate.best_pair.left.tm
        values << first_candidate.best_pair.right.tm
        values << "first"
        values << first_candidate.best_pair.product_size
#          else
#            values << "" 
      end

    end

  elsif primer3_line_1 
    values << primer3_line_1.polymorphism
    values << primer3_line_1.left_primer
    values << primer3_line_1.left_primer_snp(self) 
    values << primer3_line_1.right_primer 
    values << primer3_line_1.type.to_s 
    values << primer3_line_1.orientation.to_s      
    values << primer3_line_1.best_pair.left.tm 
    values << "NA"
    values << primer3_line_1.best_pair.right.tm

    values << "first+"
    values << primer3_line_1.best_pair.product_size
  elsif primer3_line_2 
    values << primer3_line_2.polymorphism
    values << primer3_line_2.left_primer_snp(self) 
    values << primer3_line_2.left_primer
    values << primer3_line_2.right_primer
    values << primer3_line_2.type.to_s
    values << primer3_line_2.orientation.to_s
    values << "NA"
    values << primer3_line_2.best_pair.left.tm
    values << primer3_line_2.best_pair.right.tm
    values << "second+"
    values << primer3_line_2.best_pair.product_size

  end 
  values.join(",")
end

#to_s ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 77

def to_s
  "#{gene}:#{original}#{position}#{snp}:#{snp_from.chromosome}"
end