Class: PluginIgnoreRepeated

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

Constant Summary collapse

SIZE_SEARCH_IN_IGNORE = 
15

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_ignore_repeated.rb', line 83

def self.check_params(params)
  errors=[]
                
   # self.check_param(errors,params,'fasta_file_input','String')
   self.check_param(errors,params,'blast_evalue_ignore_repeated','Float') 
   self.check_param(errors,params,'blast_percent_ignore_repeated','Integer')
   self.check_param(errors,params,'piro_repeated_start','Integer')
   self.check_param(errors,params,'piro_repeated_length','Integer')
  return errors
end

Instance Method Details

#exec_seq(seq, blast_query) ⇒ Object

Begins the plugin1’s execution to warn that there are repeated sequences, and disables all but one“



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

def exec_seq(seq,blast_query)

  $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: searching sequence repeated at input file" 

  fasta_input=@params.get_param('truncated_input_file')
  
  blast = BatchBlast.new("-db #{fasta_input}" ,'blastn'," -task blastn-short -searchsp #{SIZE_SEARCH_IN_IGNORE} -evalue #{@params.get_param('blast_evalue_ignore_repeated')} -perc_identity #{@params.get_param('blast_percent_ignore_repeated')}")  #get contaminants
  
  p_start = @params.get_param('piro_repeated_start').to_i
  p_length = @params.get_param('piro_repeated_length').to_i
  
  
  blast_table_results = blast.do_blast(seq.seq_fasta[p_start,p_length])             #rise seq to contaminants  executing over blast
  
  #blast_table_results = BlastTableResult.new(res)
  
 
   type = "ActionIgnoreRepeated"        
   
   # @stats[:rejected_seqs]={}    
     
   actions=[]     
   blast_table_results.querys.each do |query|
                                             
         # puts "BLAST IGUALES:"
         # puts res.join("\n")       
     if query.size>1   
       names = query.hits.collect{ |h| 
            if h.align_len > (p_length-2)
              h.subject_id
            end
       }
           
       names.compact!   
        
        # puts "IGUALES:" + names.size.to_s 
        #            puts names.join(',')               
        
        if !names.empty?
           names.sort!
		     
           if (names[0] != seq.seq_name)   # Add action when the sequence  is repeated 
		     #  if true 
		        a = seq.new_action(0,0,type)
		        a.message = seq.seq_name  + ' equal to ' + names[0]    
		        actions.push a
		        seq.seq_rejected=true   
		        seq.seq_rejected_by_message='repeated'
		        seq.seq_repeated=true       
		        
              # @stats[:rejected_seqs]={'rejected_seqs_by_repe' => 1}   
              add_stats('rejected_seqs','rejected_seqs_by_repe') 
               # puts "#{names[0]} != #{seq.seq_name} >>>>>>"       
		     end                                                               
       end
       
     end       
     
   end 
   
   seq.add_actions(actions)
   
end