Class: PluginLowQuality

Inherits:
Plugin
  • Object
show all
Defined in:
lib/seqtrimnext/plugins/plugin_low_quality.rb,
lib/seqtrimnext/plugins_old/plugin_low_quality_old.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_plugin_stats, #add_stats, #add_text_stats, auto_setup, #can_execute?, check_param, #do_blasts, #execute, 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 165

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)
 
  
 comment='Minimum length of a bad quality segment inside the sequence'
default_value = 8
params.check_param(errors,'min_length_inside_seq','Integer',default_value,comment)
 
  
 comment='Maximum consecutive good-quality bases between two bad quality regions'
default_value = 2
params.check_param(errors,'max_consecutive_good_bases','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_old/plugin_low_quality_old.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_old/plugin_low_quality_old.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_old/plugin_low_quality_old.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_old/plugin_low_quality_old.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_old/plugin_low_quality_old.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, blast_query) ⇒ 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 118

def exec_seq(seq,blast_query)

  if ((self.class.to_s=='PluginLowQuality') && seq.seq_qual.nil? ) 
    $LOG.debug " Quality File haven't been provided. It's impossible to execute " + self.class.to_s     
  elsif ((seq.seq_qual.size>0) && (@params.get_param('use_qual').to_s=='true'))
       
       $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: checking low quality of the sequence"
       
       min_quality=@params.get_param('min_quality').to_i
       min_length_inside_seq=@params.get_param('min_length_inside_seq').to_i
       max_consecutive_good_bases=@params.get_param('max_consecutive_good_bases').to_i
       
       type='ActionLowQuality'
       actions=[]
       
       regions=get_low_qual_regions(seq.seq_qual,min_quality,min_length_inside_seq,max_consecutive_good_bases)
       
       regions.each do |r|
         low_qual_size=r.last-r.first+1
         
         # puts "(#{low_qual_size}) = [#{r.first},#{r.last}]: #{a[r.first..r.last].map{|e| ("%2d" % e.to_s)}.join(' ')}"
        
        
        add_stats('low_qual',low_qual_size)
        
        
        # create action
        a = seq.new_action(r.first,r.last,type) # adds the correspondent action to the sequence
        actions.push a
        
        
        
       end

       # add quals
       seq.add_actions(actions)
  end       

end

#find_bounds_high_quality(sum, ini, index_window_end) ⇒ Object 



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# File 'lib/seqtrimnext/plugins_old/plugin_low_quality_old.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

#get_low_qual_regions(quals, min_value, min_region_size, max_good_quals = 2) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 72

def get_low_qual_regions(quals,min_value, min_region_size,max_good_quals=2)

  # the initial region is the whole array
  left=0
  right=quals.length-1
  # puts quals.map{|e| ("%2d" % e.to_s)}.join(' ')

  # puts "[#{left},#{right}]"

  i = 0

  from_pos=0
  regions =[]

  # get all new regions
  begin
    rstart, rend = next_low_qual_region(quals,from_pos,min_value,max_good_quals)
    if !rstart.nil?
      from_pos= rend+1

      if valid_low_qual_region?(quals,rstart,rend,min_region_size)
        regions << [rstart,rend]
      end
    end
  end while !rstart.nil?

  return regions  

end

#next_low_qual_region(quals, from_pos, min_value, max_good_quals = 2) ⇒ Object 



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

def next_low_qual_region(quals,from_pos,min_value,max_good_quals=2)

   rstart=nil
   rend=nil

   i=from_pos

   good_q=0

   # skip good values
   while (i< quals.length) && (quals[i]>=min_value)
     i +=1 
   end 

   # now we have found a bad quality, or end of sequence
   if i < quals.length
     rstart=i
     len=0

      # puts "   - [#{rstart},#{len}]"

     # continue growing while region of lowqual until more than 2 bases of good qual are found
     begin
       q=quals[i]

       if q<min_value
         len += 1
         # puts "BAD #{q}<#{min_value}"
         len += good_q
         good_q=0
       else
         good_q+=1
       end
        # puts "#{q} - q[#{rstart},#{rend}], #{good_q}"     

       i+=1
     end while (i < quals.length) && (good_q <= max_good_quals)

     rend = rstart + len -1
     # puts "#{q} - q[#{rstart},#{rend}], #{good_q}"     
   end

   return [rstart,rend]
end

#valid_low_qual_region?(quals, rstart, rend, min_region_size) ⇒ Boolean

A region is valid if it starts in 0, ends in seq.length or is big enought

Returns:

  • (Boolean) 


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# File 'lib/seqtrimnext/plugins/plugin_low_quality.rb', line 62

def valid_low_qual_region?(quals,rstart,rend,min_region_size)
  # puts [rstart,rend,0,quals.length,(rend-rstart+1)].join(';')
  # res =((rstart==0) || (rend==quals.length-1) || ((rend-rstart+1)>=min_region_size))
  # if res
  #    puts "VALID"
  # end
  return ((rstart==0) || (rend==quals.length-1) || ((rend-rstart+1)>=min_region_size))
end