gistfile1.txt

require 'logger'
require 'net/http'
require 'open-uri'

#Roshan Khan
#CS 590B
#HW4 - HMM


class Fasta
  attr_accessor :dna, :html

  def initialize(code)
    p "Retrieving Fasta for #{code}"
    @html = File.open(code).read
    @dna = html.split(/\n/)[1..-1].join
    p "Fasta retrieved, length #{@dna.length}"
    replacement = 0
    while ([email protected](/[BDEFHIJKLMNOPQRSUVWXYZ]/).nil?)
      @dna[/[BDEFHIJKLMNOPQRSUVWXYZ]/] = 'T'
      replacement += 1
    end
    p "Replaced #{replacement} proteins with T"
  end
end

class ViterbiPath
  
  STATES = ['STANDARD', 'CG_RICH']
  OBS = ['A', 'C', 'G', 'T']
  START =  {'STANDARD' , 0.9999, 'CG_RICH' , 0.0001} 
  TRANS =  {'STANDARD' , {'STANDARD' , 0.9999, 'CG_RICH' , 0.0001} , 'CG_RICH' , {'STANDARD' , 0.01, 'CG_RICH' , 0.99} }
  #TRANS =  {'STANDARD' , {'STANDARD' , 0.6, 'CG_RICH' , 0.4} , 'CG_RICH' , {'STANDARD' , 0.2, 'CG_RICH' , 0.8} }
  EMIT =   {'STANDARD' , { 'A' , 0.25, 'C' , 0.25, 'G' , 0.25, 'T',0.25 }, 'CG_RICH' ,  {'A' , 0.2, 'C' , 0.3, 'G' , 0.3, 'T',0.2} } 
  
  
  # Initalize data structure for holding calculations. States x Dna array
  def initialize (dna)
    @dna = dna
  end
  
  def traceback
    @path = []
    last_parent = ""
    # Find highest value in the last node, to see where to start trace
    if (@vit[@vit.length-1]['STANDARD'] > @vit[@vit.length-1]['CG_RICH'])
      p "Probability of this path is " + @vit[@vit.length-1]['STANDARD'].to_s
      @path << @vit[@vit.length-1]['STANDARDparent']
      lastparent = @vit[@vit.length-1]['STANDARDparent']
    else      
      p "Probability of this path is " + @vit[@vit.length-1]['CG_RICH'].to_s
      @path << @vit[@vit.length-1]['CG_RICHparent']
      lastparent = @vit[@vit.length-1]['CG_RICHparent']
    end
    
    
    # Now count back from last node - 1
    count = @vit.length - 2  
    while (count >= 0)
      # New path is viterbi sequence position, and look up parent value
      @path << @vit[count][lastparent+'parent']
      lastparent = @vit[count][lastparent+'parent']
      count -= 1
    end
    @path = @path.reverse
  end
  
  def train
    p "Initiating training"
    
    tc = { "STANDARD", {"STANDARD", 0.0, "CG_RICH", 0.0}, "CG_RICH", {"STANDARD", 0.0, "CG_RICH", 0.0} }
    ec = {'STANDARD' , { 'A' , 0.0, 'C' , 0.0, 'G' , 0.0, 'T',0.0 }, 'CG_RICH' ,  {'A' , 0.0, 'C' , 0.0, 'G' , 0.0, 'T',0.0} } 
    
    cur = @path[1]
    
    for i in ([email protected])    
      tc[cur][@path[i]] += 1
      ec[cur][@dna[i].chr] += 1      
      cur = @path[i] 
    end
    
    standard_total = tc["STANDARD"]["STANDARD"] + tc["STANDARD"]["CG_RICH"]
    cg_total = tc["CG_RICH"]["CG_RICH"] + tc["CG_RICH"]["STANDARD"]
    
    TRANS["STANDARD"]["STANDARD"] = tc["STANDARD"]["STANDARD"] / standard_total
    TRANS["STANDARD"]["CG_RICH"] = tc["STANDARD"]["CG_RICH"] / standard_total
    TRANS["CG_RICH"]["STANDARD"] = tc["CG_RICH"]["STANDARD"] / cg_total
    TRANS["CG_RICH"]["CG_RICH"] = tc["CG_RICH"]["CG_RICH"] / cg_total
    
    s_total = ec["STANDARD"]["A"] + ec["STANDARD"]["C"] + ec["STANDARD"]["G"] + ec["STANDARD"]["T"]
    g_total = ec["CG_RICH"]["A"] + ec["CG_RICH"]["C"] + ec["CG_RICH"]["G"] + ec["CG_RICH"]["T"]
    
    EMIT["STANDARD"]["A"] = ec["STANDARD"]["A"] / s_total
    EMIT["STANDARD"]["C"] = ec["STANDARD"]["C"] / s_total
    EMIT["STANDARD"]["G"] = ec["STANDARD"]["G"] / s_total
    EMIT["STANDARD"]["T"] = ec["STANDARD"]["T"] / s_total
    
    EMIT["CG_RICH"]["A"] = ec["CG_RICH"]["A"] / g_total
    EMIT["CG_RICH"]["C"] = ec["CG_RICH"]["C"] / g_total
    EMIT["CG_RICH"]["G"] = ec["CG_RICH"]["G"] / g_total
    EMIT["CG_RICH"]["T"] = ec["CG_RICH"]["T"] / g_total
    
    p "New parameters are"
    p "TRANSITION"
    p TRANS 
    p "EMISSION"
    p EMIT
  end
  
  # 1->1 = 1->1 / 1->1+1->2
  # 1->2 = 1->2 / 1->1+1->2
  # 2->1 = 2->1/ 2->1 + 2->2
  # 2->2 = 2->2 / 2->2 + 2->2
  # same thing for distribution
  
  def print_cg_areas
    in_cg = false
    start_node = 0
    len = 0
    hits = 0
    @path.each_with_index do |state, index|
      if (state == "CG_RICH")
        if (in_cg == true)
          len+=1
        else
          in_cg = true
          start_node = index
          len=1
        end
      else
        if (in_cg == true)
          hits += 1 
          # FINISHED A CG_RICH AREA - PRINT THIS
          p "CG_Rich area from #{start_node} to #{start_node + len} which is #{len} bp long."
          odds = @vit[index]['CG_RICH']
        end
        in_cg = false
        len = 0
      end
    end
    p "Total number of hits in this sequence is #{hits}"
  end
  
  def longest_rich_area
    in_cg = false
    start_node = 0
    longest_start = 0
    longest_len = 0
    len = 0
    @path.each_with_index do |state, index|
      if (state == "CG_RICH")
        if (in_cg == true)
          len+=1
        else
          in_cg = true
          start_node = index 
          len=1
        end
      else
        in_cg = false
        len = 0
      end
      
      if (longest_len < len)
        longest_len = len
        longest_start = start_node
      end 
    end
    
    p longest_len
    p longest_start
    #p @path[longest_start...longest_start+longest_len]
  end
    
  #TODO: Change this function name
  # Calculate state values across all nodes in the chain
  def predict()
    @vit = Array.new()
    @vit << {}
    for state in STATES
      @vit[0][state] = Math.log(START[state] * EMIT[state][@dna[0].chr])
    end
    start = Time.now
    for t in ([email protected])
      @vit << {}
      if (t % 100000 == 0)
        p "Completed #{t} in #{Time.now - start} seconds"
      end
      for y in STATES
        values = []
        for y0 in STATES
          values << [@vit[t-1][y0] + Math.log(TRANS[y0][y] * EMIT[y][@dna[t].chr]), y0]
        end
        @vit[t][y] = values.max[0]
        @vit[t][y + 'parent'] = values.max[1]
      end  
    end
  end
end

if __FILE__ == $0
  f = Fasta.new(ARGV[0])
  vp = ViterbiPath.new(f.dna)
  (0...10).each do |i|
    p "---------------------------- ITERATION #{i+1} ----------------------------"
    vp.predict
    vp.traceback
    vp.print_cg_areas
    vp.train
  end
end