Class: SeqtrimWorker

Inherits:
ScbiMapreduce::Worker
  • Object
show all
Defined in:
lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb

Instance Method Summary collapse

Instance Method Details

#add_output_data(obj) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 104

def add_output_data(obj)
   obj.output_text=[]
   
 obj.each do |seq|
    obj.output_text << seq.to_text
       write_seq_to_files(obj.output_files,seq, obj.stats)
 end
 
   # @remove seqs since they are not needed anymore to write output files
   obj.remove_all_seqs
end

#add_stat(stats, key, subkey, value, count = 1) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 116

def add_stat(stats,key,subkey,value,count=1)
 
 stats[key]={} if !stats[key]
  stats[key][subkey]={} if !stats[key][subkey]
  stats[key][subkey][value]=0 if !stats[key][subkey][value]
  
 stats[key][subkey][value]+=count
end

#closing_worker ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 99

def closing_worker
   
end

#get_file(files, fn) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 288

def get_file(files,fn)
 res=files[fn]
 
 if !res
   files[fn]=[]
   res=files[fn]
  end
  
  return res
end

#json_file(files) ⇒ Object

ACCESS TO FILES



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 259

def json_file(files)
   return get_file(files,File.join(OUTPUT_PATH,'results.json'))
end

#low_complexity_file(files, dir_name, file_name) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 276

def low_complexity_file(files, dir_name, file_name)
  return get_file(files,File.join(OUTPUT_PATH,dir_name,'low_complexity_'+file_name+'.fastq'))
end

#low_sffinfo_file(files, dir_name, file_name) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 284

def low_sffinfo_file(files, dir_name, file_name)
  return get_file(files,File.join(OUTPUT_PATH,dir_name,'low_complexity_sff_info_'+file_name+'.txt'))
end

#paired_file(files, dir_name, file_name) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 272

def paired_file(files, dir_name, file_name)
  return get_file(files,File.join(OUTPUT_PATH,dir_name,'paired_'+file_name+'.fastq'))
end

#process_object(obj) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 56

def process_object(obj)
        running_seqs=SequenceGroup.new(obj)
        
       # execute plugins
       @plugin_manager.execute_plugins(running_seqs)
       
       # add output data
        add_output_data(running_seqs)
       
     return running_seqs
end

#receive_initial_config(obj) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 68

def receive_initial_config(obj)

# Reads the parameters
$WORKER_LOG.info "Params received"
#       @params = Params.new(params_path)
@params = obj

@use_qual=@params.get_param('use_qual')
@use_json=@params.get_param('use_json')
end

#rejected_output_file(files) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 263

def rejected_output_file(files)
   return get_file(files,File.join(OUTPUT_PATH,'rejected.txt'))
end

#sequence_file(files, dir_name, file_name) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 268

def sequence_file(files, dir_name, file_name)
   return get_file(files,File.join(OUTPUT_PATH,dir_name,'sequences_'+file_name+'.fastq'))
end

#sffinfo_file(files, dir_name, file_name) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 280

def sffinfo_file(files, dir_name, file_name)
  return get_file(files,File.join(OUTPUT_PATH,dir_name,'sff_info_'+file_name+'.txt'))
end

#starting_worker ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 79

def starting_worker

      # $WORKER_LOG.level = Logger::ERROR
      $WORKER_LOG.level = Logger::WARN
    $WORKER_LOG.info "Loading actions"

    @action_manager = ActionManager.new

    $WORKER_LOG.info "Loading plugins"
    @plugin_list = @params.get_param('plugin_list') # puts in plugin_list the plugins's array
    $WORKER_LOG.info "PLUGIN LIST:" + @plugin_list
    
    @plugin_manager = PluginManager.new(@plugin_list,@params) # creates an instance from PluginManager. This must storage the plugins and load it    

rescue Exception => e
  puts (e.message+ e.backtrace.join("\n"))

end

#write_seq_to_files(files, seq, stats) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 125

def write_seq_to_files(files,seq, stats)
   # puts stats.to_json
   
   dir_name,file_name=seq.get_file_tag_path
   # puts File.join(dir_name,'sequences_'+file_name)
   
   # get current inserts
   inserts = seq.get_inserts
   
   # qualities are optional
   if @use_qual
     qual_inserts = seq.get_qual_inserts
   end
   
   # save json if necessary
   if @use_json
     json_file(files)<< seq.to_json
   end
   
   # find mids
   mid = seq.get_actions(ActionMid).first
   
   if (seq.seq_rejected)           # sequence rejected
   
    #save to rejected sequences 
     message = seq.seq_rejected_by_message 
     rejected_output_file(files)<<('>'+seq.seq_name+ ' ' + message)
     
     add_stat(stats,'sequences','rejected',seq.seq_rejected_by_message)
     add_stat(stats,'sequences','count','rejected')
    

   elsif (inserts.empty?)  #sequence with no inserts
     message = 'No valid inserts found'
     rejected_output_file(files)<<('>'+seq.seq_name+ ' ' + message)
     
     add_stat(stats,'sequences','rejected',message)
     add_stat(stats,'sequences','count','rejected')
     
elsif (inserts.count == 2) # sequence with two inserts  = PAIRED SEQUENCES
     add_stat(stats,'sequences','count','output_seqs_paired')

     # TODO - Add this stats to full stats
     # @@full_stats.add_stats({'sequences' => {'paired' => {'count' => 1}}})
    
  if (mid.nil? || (mid.message=='no_MID') ) # without mid
    mid_id = 'no_MID'
    mid_message = ' No MID found'
  else
    mid_id = mid.tag_id
    mid_message=''
    if mid_id != mid_message
      mid_message = ' '+mid.message
    end
  end

     # fasta_file = get_paired_file(mid_id)

     n="#{seq.seq_name}_left"
     c="template=#{seq.seq_name} dir=R library=#{mid_id}"
     f=inserts[0].reverse.tr('actgACTG','tgacTGAC')
     q=[]
     if @use_qual
         q=qual_inserts[0].reverse          
      end   

     paired_file(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c)
     
     
     n="#{seq.seq_name}_right"
     c="template=#{seq.seq_name} dir=F library=#{mid_id}"
     f=inserts[1]
     q=[]
     if @use_qual
        q=qual_inserts[1]
      end
     
     paired_file(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c)
     
     
   elsif (inserts.count == 1) # sequence with one insert

  if (mid.nil? || (mid.message=='no_MID') ) # without mid
    mid_id = 'no_MID'
    mid_message = ' No MID found'
  else
    mid_id = mid.tag_id
    mid_message=''
    if mid_id != mid_message
      mid_message = ' '+mid.message
    end
  end

    # save fasta and qual in no MID file
     has_low_complexity = seq.get_actions(ActionLowComplexity)
     
     if has_low_complexity.empty?
       add_stat(stats,'sequences','count','output_seqs')
       
       # fasta_file = get_sequence_file(mid_id)
       # sff_file=get_sffinfo_file(mid_id)
       fasta_file=sequence_file(files,dir_name,file_name)
       sff_file=sffinfo_file(files,dir_name,file_name)
     else
       add_stat(stats,'sequences','count','output_seqs_low_complexity')
       
       # fasta_file = get_low_complexity_file(mid_id)
       # sff_file=get_low_sffinfo_file(mid_id)
       fasta_file=low_complexity_file(files,dir_name,file_name)
       sff_file=low_sffinfo_file(files,dir_name,file_name)
     end
     
     q=[]
     if @use_qual
       q=qual_inserts[0]
  end
     
     n=seq.seq_name
     c=mid_message
     f=inserts[0]
     
     fasta_file << FastqFile.to_fastq(n,f,q,c)
     
     inserts_pos = seq.get_actions(ActionInsert)
     
     sff_file<< "#{n} #{inserts_pos[0].start_pos+1} #{inserts_pos[0].end_pos+1}"
     
   end
  
end