Method: PluginLowQuality#exec_seq

Defined in:
lib/seqtrimnext/plugins/plugin_low_quality.rb,
lib/seqtrimnext/plugins_old/plugin_low_quality_old.rb

#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