Module: MS::Rtgenerator

Defined in:
lib/ms/rt/rtgenerator.rb

Class Method Summary collapse

Class Method Details

.generateRT(one_d, db) ⇒ Object 



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# File 'lib/ms/rt/rtgenerator.rb', line 13

def generateRT(one_d,db)
  prog = Progress.new("Generating retention times:")
  @r_times = Sim_Spectra.r_times

  # Gets retention times from the weka model
  MS::Weka.predict_rts(db)
  MS::Weka.predict_ints(db)


  #-----------------------------------------------------------------
  num = 0
  
  max_rt = 4*(@r_times.max/5)
  r_end = max_rt + (@r_times.max/5)/2
  r_start = @r_times.max/5
  peps = db.execute "SELECT Id,p_rt,abu,seq FROM peptides"
  total = peps.size
  step = total/100.0
  peps.each do |pep|
    ind = pep.delete_at(0)
    init_p_rt = pep[0]
    abu = pep[1]
    seq = pep[2]
    pep_p_rt = nil
    pep_p_rt_i = nil
    if ind > step * (num + 1)
      num = (((ind+1)/total.to_f)*100).to_i
      prog.update(num)
    end


    #Fit retention times into scan times
    p_rt = init_p_rt * 10**-2
    percent_time = p_rt 
    sx = RThelper.gaussian(percent_time,0.5,0.45,1.0) * Math.sqrt(abu) #need to figure out what these values should be
	

    if p_rt > 1
      pep_p_rt = @r_times.find {|i| i >= r_end}
      pep_p_rt_i = @r_times.index(pep_p_rt)
    else
      pep_p_rt = @r_times.find {|i| i >= (p_rt * max_rt)}
      pep_p_rt_i = @r_times.index(pep_p_rt)
    end
    
    a = nil
    b = nil

    if pep_p_rt == nil
      puts "\n\n\t#{seq} TIME-> #{p_rt*max_rt} :: Peptide not predicted in time range: try increasing run time\n\n."
    else

      #Give peptide retention times
      head_length = nil
      tail_length = nil
      if one_d
        head_length = 300.0
        tail_length = 701
      else
        head_length = 100.0 * sx
        tail_length = 300 * sx
      end

      a = @r_times.find {|i| i >= (pep_p_rt-head_length)}
      b = @r_times.find {|i| i >= (pep_p_rt+tail_length)}
      a = @r_times.index(a)
      b = @r_times.index(b)

      if a == nil
        a = @r_times[0]
      end

      if b == nil
        b = @r_times[@r_times.length-1]
      end

    end
    db.execute "UPDATE peptides SET p_rt=#{pep_p_rt},p_rt_index=#{pep_p_rt_i},sx=#{sx},rt_a=#{a},rt_b=#{b} WHERE Id='#{ind}'"
  end
  #-----------------------------------------------------------------
  prog.finish!
end