Module: Bio::DB::Primer3

Defined in:
lib/bio/db/primer3.rb

Defined Under Namespace

Classes: KASPContainer, Primer, Primer3Exception, Primer3Record, PrimerPair, SNP

Class Method Summary collapse

Class Method Details

.prepare_input_file(file, opts2 = {}) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 19

def self.prepare_input_file(file, opts2={})
 opts = {
  :primer_product_size_range => "50-150" ,
  :primer_max_size => 25 , 
  :primer_lib_ambiguity_codes_consensus => 1,
  :primer_liberal_base => 1, 
  :primer_num_return => 5,
  :primer_explain_flag => 1,
  :primer_thermodynamic_parameters_path => File.expand_path(File.dirname(__FILE__) + '../../../../conf/primer3_config/') + '/'
  }.merge(opts2)
  
  opts.each do |key,value|
    file.puts "#{key.to_s.upcase}=#{value}\n"
  end
  # file.puts "="
end

.read_primer_preferences(file, defaults) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 6

def self.read_primer_preferences(file, defaults)

  File.open(file) do |f|
    f.each_line do | line | 
      line.chomp!
      arr = line.split("=")
      defaults[arr[0].downcase.to_sym] = arr[1];
    end
  end

  return defaults
end

.run(opts = {}) ⇒ Object 



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# File 'lib/bio/db/primer3.rb', line 36

def self.run(opts={})
  puts "Primer3.run running..."

  f_in=opts[:in]
  f_out=opts[:out]
  opts.delete(:in)
  opts.delete(:out)
  primer_3_in = File.read(f_in)
  status = systemu "primer3_core", 0=>primer_3_in, 1=>stdout='', 2=>stderr=''
  # $stderr.puts cmdline
  if status.exitstatus == 0
    File.open(f_out, 'w') { |f| f.write(stdout) }
  else
    raise Primer3Exception.new(), "Error running primer3. Command line was 'primer3_core'\nPrimer3 STDERR was:\n#{stderr}"
  end
end