Class: Bio::DB::Primer3::KASPContainer

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#line_1 ⇒ Object

Returns the value of attribute line_1.



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# File 'lib/bio/db/primer3.rb', line 753

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 753

def line_2
  @line_2
end

#scores ⇒ Object

Returns the value of attribute scores.



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# File 'lib/bio/db/primer3.rb', line 755

def scores
  @scores
end

#snp_hash ⇒ Object

Returns the value of attribute snp_hash.



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# File 'lib/bio/db/primer3.rb', line 754

def snp_hash
  @snp_hash
end

Instance Method Details

#add_primers_file(filename) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 787

def add_primers_file(filename)
  #primer3record.scores = @scores if @scores
  Primer3Record.parse_file(filename, scores: @scores) do | primer3record |
    current_snp = @snp_hash["#{primer3record.snp.to_s}:#{primer3record.chromosome}"]
    current_snp.add_record(primer3record)
  end
end

#add_snp(snp_in) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 766

def add_snp(snp_in) 
  #TODO: Here we need to also copy the errors that will be printed. 
  @snp_hash=Hash.new unless @snp_hash
  snp = SNP.new
  snp.gene = snp_in.gene
  snp.original = snp_in.original
  snp.primer3_errors = Set.new snp_in.errors
  snp.position = snp_in.position
  snp.snp = snp_in.snp
  snp.repetitive = snp_in.repetitive
  #puts snp_in.inspect
  snp.hit_count = snp_in.hit_count
  snp.snp_type  = snp_in.snp_type
  snp.line_1 = @line_1
  snp.line_2 = @line_2 
  snp.snp_from = snp_in
  snp.regions = snp_in.exon_list.values.collect { |x|  x.collect {|y| y.target_region.to_s }}
  @snp_hash[snp.to_s] = snp
  snp
end

#add_snp_file(filename) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 757

def add_snp_file(filename)
  @snp_hash=Hash.new unless @snp_hash
  SNP.parse_file(filename) do |snp|
    @snp_hash[snp.to_s] = snp
    snp.line_1 = @line_1
    snp.line_2 = @line_2
  end
end

#print_primers ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 795

def print_primers
  str = ""
  snp_hash.each do |k, snp|
    str << snp.print_primers << "\n"
  end
  return str
end

#print_primers_with_tails(tail_a: "GAAGGTCGGAGTCAACGGATT", tail_b: "GAAGGTGACCAAGTTCATGCT") ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 803

def print_primers_with_tails(tail_a: "GAAGGTCGGAGTCAACGGATT", tail_b: "GAAGGTGACCAAGTTCATGCT")
  str = ""
  snp_hash.each do |k, snp|  
    if snp.found_primers?
      str << snp.gene << snp.original << "_1st\t" << tail_a << snp.first_primer  << "\n"
      str << snp.gene << snp.snp      << "_2nd\t" << tail_b << snp.second_primer << "\n"
      str << snp.gene                 << "_common\t"        << snp.common_primer << "\n"
    end
  end
  return str
end