Class: PluginLowQuality

Inherits:
Plugin
  • Object
show all
Defined in:
lib/seqtrimnext/plugins/plugin_low_quality.rb

Overview

Inherit: Plugin

Instance Attribute Summary

Attributes inherited from Plugin

#stats

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Plugin

#add_stats, #add_text_stats, auto_setup, check_param, get_graph_filename, get_graph_title, graph_ignored?, ignored_graphs, #initialize, #merge_hits, #overlapX?, plot_setup, valid_graphs

Constructor Details

This class inherits a constructor from Plugin

Class Method Details

.check_params(params) ⇒ Object

Returns an array with the errors due to parameters are missing



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 374

def self.check_params(params) 
  
  errors=[]
  
 	comment='Minimum quality value for every nucleotide'
default_value = 20
params.check_param(errors,'min_quality','Integer',default_value,comment)

 	comment='Quality window for scanning low quality segments'
default_value = 15
params.check_param(errors,'window_width','Integer',default_value,comment)
 

  
  return errors
end

Instance Method Details

#add_action_after_high_qual(p_begin, p_end, actions, seq) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 237

def add_action_after_high_qual(p_begin,p_end,actions,seq)

  action_size = seq.insert_end-p_end
  if action_size>=(@window/2)


     # puts "action_SIZE2 #{action_size} > #{@window/2}"

     if ((p_end<seq.seq_fasta.size-1) && (action_size>0) )  #if there is action before the high qual part 
       # it's created an action before of the high quality part
       a = seq.new_action(p_end-seq.insert_start+1,seq.seq_fasta.size-1,"ActionLowQuality") # adds the ActionInsert to the sequence before adding the actionMid

       actions.push a   
     end 
   end 
end

#add_action_before_high_qual(p_begin, p_end, actions, seq, start) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 220

def add_action_before_high_qual(p_begin,p_end,actions,seq,start)

  action_size = p_begin-1
  if action_size>=(@window/2)  


    # puts "action_SIZE1 #{action_size} > #{@window/2}"

    if ( (p_begin>0) && (action_size>0) )  #if there is action before the high qual part 
      # it's created an action before of the high quality part
      a = seq.new_action(start ,p_begin-1,"ActionLowQuality") # adds the ActionInsert to the sequence before adding the actionMid
      # puts " new low qual start: #{start}  = #{a.start_pos} end: #{p_begin} -1 = #{a.end_pos}"
      actions.push a   
    end 
  end             
end

#create_sum_window(qual, ini, index_window_end) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 16

def create_sum_window(qual,ini,index_window_end)

  # puts "--------index w #{index_window_end}" 
  sum=[] 
  i=ini  
  # puts "#{i} #{index_window_end}"
  while (i<=index_window_end) # initialize sum                                  
    sum[i]=0 
    i += 1
  end
  # puts " contenido de sum" + sum.join.to_s  + " i index_window_end  window #{i} #{index_window_end} #{@window}" 

  i=ini
  while (i<ini+@window)

    sum[ini] += qual[i] 
    i+=1
  end                                           


  i=ini+1 

  while (i<=index_window_end)            

    sum[i]=sum[i-1]-qual[i-1]+qual[i+@window-1]
    i+=1

  end   

  # puts '2____' + sum.join(',') + 'pos sum' + ini.to_s    

  return sum 

end

#cut_fine_bounds(qual, new_start, new_end) ⇒ Object

cuts fine the high quality bounds



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 138

def cut_fine_bounds(qual,new_start,new_end)   
  # puts "  ççççççççççççççç #{new_start+@window} >= #{new_end} " 
  # puts " #{new_start} #{new_end} .o.o.o.o.o.o.o.o1"
  # cut it fine

   one_ok = 0         

    i=@window-1
    # puts " qual[new_start+i] new_start #{new_start} i #{i} = #{new_start+i} qual.size #{qual.size}"
    while (i>=0) 
        if (qual[new_start+i] < @low) 
            break if one_ok
        else 
            one_ok = 1
        end    
        i-=1
    end
    new_start += i+1
    oneOk = 0  
    i=0
    while (i<@window) 
        if (qual[new_end+i] < @low) 
            break if oneOk
        else 
            oneOk = 1
        end  
        i+=1
    end
    new_end += i-1 
    # puts "6b  new_start #{new_start} new-end #{new_end}"  

  # puts " #{new_start} #{new_end} .o.o.o.o.o.o.o.o2"
  return new_start, new_end

end

#cut_fine_bounds_short(qual, new_start, new_end) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 108

def cut_fine_bounds_short(qual,new_start,new_end)

    i=0                    
    # puts " qual[new_start+i] new_start #{new_start} i #{i} = #{new_start+i} qual.size #{qual.size}"
    while (i<@window)
      if (qual[new_start+i]>=@low)
        break
      end    
      i+=1
    end  
    new_start +=i 
    # puts "#{new_start} ***********"

    i=@window -1
    while (i>=0)  
      if (qual[new_end+i]>=@low)    
        break            
      end
      i-=1            
    end     
    new_end += i
    # puts "6a new_start #{new_start} new-end #{new_end}"     
    
     # puts " #{new_start} #{new_end} .o.o.o.o.o.o.o.o2 short"    
    return new_start, new_end  

end

#exec_seq(seq) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 276

def exec_seq(seq)

  if ((self.class.to_s=='PluginLowQuality') && seq.seq_qual.nil? ) 
    $LOG.error " Quality File haven't been provided. It's impossible to execute " + self.class.to_s     
  elsif (seq.seq_qual.size>0)
    $LOG.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: checking low quality of the sequence"    

    @low=@params.get_param('min_quality').to_i

    if @params.get_param('window_width').to_i>seq.seq_fasta.length   
      @window=seq.seq_fasta.length   
    
    else 
      @window=@params.get_param('window_width').to_i  
    
    end 
    @cut_off=@window*@low   
                                        
    type='ActionLowQuality' 
    low_qual=0
    actions=[] 
    
    p_begin,p_end =0,-1 # positions from high quality bounds    
                             
    # @stats[:low_qual]={}    
    # @stats['low_qual']={} 
    
    
    while ((p_begin>=0)  && (p_end + 1 < seq.seq_qual.size) ) 
      
      
      p_begin_old,p_end_old= p_begin, p_end
      p_begin,p_end = find_high_quality(seq.seq_qual,p_end+1)  
      # entra=(p_begin>0) or (p_end_old<0)
      #         
      # puts "high ini fin #{p_begin} #{p_end} ini-old fin-old  #{p_begin_old} #{p_end_old} __ ___ ___ ___1"     
      
      if ((p_begin>0) && (p_begin-p_end_old-1>=@window/2)) #if we have found the high quality part, and  the low quality part has enough size 
         # it's created an action before of the high quality part 
         add_action_before_high_qual(p_begin,p_end,actions,seq,p_end_old+1) 
         # puts "low1 ini fin  #{p_end_old+1} #{p_begin-1} = #{p_begin-1-p_end_old-1+1}"     
         low_qual = p_begin-1-p_end_old-1 + 1 
         
         add_stats('low_qual',low_qual)
         # @stats[:low_qual]={low_qual => 1} 
          
      end
      
      # puts "-----ññññ----- high quality  #{p_begin}   #{p_end}+#{seq.insert_start} seq size #{seq.seq_fasta.size}"   

    end
     
    # puts "high [#{p_begin}, #{p_end}] old [#{p_begin_old}, #{p_end_old}] size #{seq.seq_qual.size}"   
    if ((p_begin>=0) && (p_end+1<seq.seq_qual.size))  #if we have found the high quality part 
       
       # it's created an action after of the high quality part     
       add_action_after_high_qual(p_begin,p_end,actions,seq) 
       # puts "low2 ini fin #{p_end+1} #{seq.seq_fasta.size-1}  = #{seq.seq_fasta.size-1-p_end-1+1}"
       low_qual = seq.seq_fasta.size-1 - p_end-seq.insert_start-1 + 1
       # if @stats[:low_qual][low_qual].nil?
       #              @stats[:low_qual][low_qual] = 0
       #           end
       #           @stats[:low_qual][low_qual] += 1  
       add_stats('low_qual',low_qual) 
       # @stats[:low_qual]={low_qual => 1}    
    end                                     

    # puts "-----ññññ----- high quality  #{p_begin}   #{p_end}"  

    
    if p_end<0 and p_end_old #add action low qual to all the part      
      a = seq.new_action(p_end_old+1 ,seq.seq_fasta.size-1,"ActionLowQuality") # adds the ActionInsert to the sequence before adding the actionMid
      # puts "new low qual start: #{p_end_old+1} end: #{seq.seq_fasta.size-1} = #{seq.seq_fasta.size-1 - p_end_old-1 + 1}" 
      low_qual = seq.seq_fasta.size-1 - p_end_old-1 + 1 
      
       # if @stats[:low_qual][low_qual].nil?
       #             @stats[:low_qual][low_qual] = 0
       #          end
       #          @stats[:low_qual][low_qual] += 1   
      add_stats('low_qual',low_qual) 
      # @stats[:low_qual]={'low_qual' => 1} 
       
      actions.push a
    end
    
    # puts "------- ADDING ACTIONs LOW QUAL #{actions.size}"    
    seq.add_actions(actions)
  end       

end

#execute(seqs) ⇒ Object

Begins the plugin1’s execution whit the sequence “seq” Creates an action by each subsequence with low quality to eliminate it A subsequence has low quality if (the add of all its qualitis < subsequence_size*20)

Creates the qualities windows from the sequence, looks for the subsequence with high quality and mark, with an action, the before part to the High Quality Subsequence like a low quality part Finally mark, with an action, the after part to the High Quality Subsequence like a low quality part



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 269

def execute(seqs)
 seqs.each do |s|
     exec_seq(s)
  end
end

#find_bounds_high_quality(sum, ini, index_window_end) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 51

def find_bounds_high_quality(sum,ini,index_window_end) 

  new_start = -1
  new_end = -1
  
# puts " ini #{ini} iwe #{index_window_end}"
# puts "ini #{ini} index_window_end #{index_window_end} sum[ini] #{sum[ini]} cut_off #{@cut_off} suma #{sum.size} " 
 if (ini>index_window_end) 
     temp_start= ini
     # new_start, new_end = temp_start, index_window_end 
     new_end = index_window_end # para que no crea que no hay alta calidad, sino que hemos sobrepasado el indice final de la ventana
       # new_start, new_end = index_window_end, index_window_end 
 end   
# puts " temp_start #{temp_start}" if (ini>index_window_end)
temp_start=((ini<=index_window_end) && (sum[ini]>=@cut_off))? ini : -1    

  i=ini+1
  while (i<=index_window_end)
    if (sum[i]>=@cut_off)  
      if (temp_start<0)
         temp_start=i  #just in! 
         # puts "just in ---- #{sum[i]}>= cut off #{@cut_off} pos #{temp_start}"   
      end

    else 
        # puts "sum #{sum[i]} < cut off "
        if(temp_start>=0)              #just out!   
          # puts "update #{sum[i]}< cut off #{@cut_off} pos #{i}.if #{i-1} - #{temp_start} > #{new_end} - #{new_start}"
          if (((i-1-temp_start)>=(new_end-new_start)))   
            new_start,new_end=temp_start,i-1 
            # puts "just out ---- new start,new_end = #{temp_start}, #{i-1}  index_window_end = #{index_window_end}"   
          end
          temp_start= -1 
        end
    end
    i+=1  


  end 
  # puts "4 temp_start #{temp_start} new_start #{new_start} new-end #{new_end}"  

  if (temp_start != -1)   # finished while ok           
    # puts "4 #{index_window_end} - #{temp_start} > #{new_end} - #{new_start}"
      if ((index_window_end- temp_start) >= (new_end-new_start)) #put the end of the window at the end of sequence
          new_start, new_end = temp_start, index_window_end     #-1
      end
  end  

  # puts "5 temp_start #{temp_start} new_start #{new_start} new-end #{new_end}"   
  
  # puts  " newstart  #{new_start} newend #{new_end}" 
 
  return new_start,new_end 
 

end