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, #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

#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)
       
       $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

#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