Class: SeqtrimWorkManager

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

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.end_work_manager ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 88

def self.end_work_manager

  puts "FULL STATS:\n" +JSON.pretty_generate(@@full_stats)

  f = File.open(STATS_PATH,'w')
  f.puts JSON.pretty_generate(@@full_stats)
  f.close

  r=File.read(STATS_PATH)

  stats=JSON::parse(r)


  gs=GraphStats.new(stats)

  #gs=GraphStats.new(@@full_stats)


  #close all files

  # @@fqr.close
  if @@use_json
    @@json_output.close
  end
  @@errors_file.close
  # @@rejected_output_file.close

  # @@paired_output_files.each do |k,file|
  #   file.close
  # end

  @@files.each do |k,file|
    file.close
  end

  # @@paired_qual_output_files.each do |k,file|
  #            file.close
  # end

  # @@sequences_output_files.each do |k,file|
  #   file.close
  # end
  #
  # @@low_complexity_output_files.each do |k,file|
  #   file.close
  # end
  #
  # @@sffinfo_files.each do |k,file|
  #   file.close
  # end
  #
  # @@low_sffinfo_files.each do |k,file|
  #   file.close
  # end


  # @@qual_output_files.each do |k,file|
  #  file.close
  # end

  # more than one MID found
  # if @@full_stats['mid_id'] && @@full_stats['mid_id'].count>1
  #
  # end

  if File.exists?('scbi_drb_checkpoint')
    File.delete('scbi_drb_checkpoint')
  end
end

.init_work_manager(sequence_reader, params, chunk_size = 100, use_json = false) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 16

def self.init_work_manager(sequence_reader, params, chunk_size = 100, use_json=false)
  @@full_stats={}
  @@params= params
  @@exit = false

  @@chunk_size = chunk_size


  # puts "CHECKPOINT: #{self.checkpoint}\n"*20

  checkpoint_exists=File.exists?('scbi_drb_checkpoint')

  # @@use_qual = !qual_path.nil? and File.exists?(qual_path)
  @@open_mode='w'
  if checkpoint_exists
    @@open_mode = 'a'
    if File.exists?(STATS_PATH)
      # load stats
      text = File.read(STATS_PATH)

      # wipe text
      # text=text.grep(/^\s*[^#]/).to_s

      # decode json
      @@full_stats = JSON.parse(text)
    end
  end

  #open input file
  @@fqr=sequence_reader

  # @@use_qual = @@fqr.with_qual?
  # @@use_json = use_json

  @@params.set_param('use_qual',@@fqr.with_qual?)
  @@params.set_param('use_json',use_json)

  @@use_json=use_json

  @@fqr.rewind

  # open output files

  if !Dir.exists?(OUTPUT_PATH)
    Dir.mkdir(OUTPUT_PATH)
  end

  @@files={}

  # @@rejected_output_file=File.open(File.join(OUTPUT_PATH,'rejected.txt'),@@open_mode)

  # seqs_with_errors
  @@errors_file=File.open('errors.txt',@@open_mode)

  if @@use_json
    @@json_output=File.open('results.json',@@open_mode)
  end

  @@json_separator=''

  @@paired_output_files={}

  @@sequences_output_files={}

  @@low_complexity_output_files={}

  @@sffinfo_files={}

  @@low_sffinfo_files={}

end

Instance Method Details

#error_received(worker_error, obj) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 159

def error_received(worker_error, obj)
  @@errors_file.puts "Error while processing object #{obj.inspect}\n" + worker_error.original_exception.message + ":\n" +worker_error.original_exception.backtrace.join("\n")
  @@errors_file.puts "="*60
end

#get_file(file_name) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 313

def get_file(file_name)
  res_file = @@files[file_name]

  # if file is not already open, create it
  if res_file.nil?
    # create dir if necessary
    dir = File.dirname(file_name)
    if !File.exists?(dir)
      FileUtils.mkdir_p(dir)
    end

    # open file
    res_file=File.open(file_name,@@open_mode)

    # save it in hash for next use
    @@files[file_name]=res_file
  end

  return res_file
end

#load_user_checkpoint(checkpoint) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 172

def load_user_checkpoint(checkpoint)

  # reset count stats since they are repeated by checkpointing

  # if @@full_stats['sequences'] && @@full_stats['repeated']
  #   @@full_stats['sequences']['count']['repeated']=0
  # end
  #
  # if @@full_stats['sequences'] && @@full_stats['processed']
  #   @@full_stats['sequences']['processed']['count']=0
  # end
  #
  # if @@full_stats['sequences'] && @@full_stats['total']
  #   @@full_stats['sequences']['total']['count']=0
  # end

  super
  # return checkpoint
end

#next_work ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 216

def next_work

  if @@exit
    return nil
  end

  begin

    n,f,q,c = @@fqr.next_seq

    if !n.nil? && @@params.repeated_seq?(n)
      @@full_stats.add_stats({'sequences' => {'count' => {'rejected' => 1}}})
      @@full_stats.add_stats({'sequences' => {'rejected' => {'repeated' => 1}}})

      get_file(File.join(OUTPUT_PATH,'rejected.txt')).puts('>'+n+ ' repeated')
      
    end
    
    if !n.nil?
      @@full_stats.add_stats({'sequences' => {'count' => {'input_count' => 1}}})
    end
  end while (!n.nil? && @@params.repeated_seq?(n))

  if !n.nil?
    return SequenceWithAction.new(n,f.upcase,q,c)
  else
    return nil
  end


end

#save_files(obj) ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 305

def save_files(obj)
  files=obj.output_files
  files.each do |file_name,content|
    f=get_file(file_name)
    f.puts content
  end
end

#save_user_checkpoint ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 192

def save_user_checkpoint

  f = File.open(STATS_PATH,'w')
  f.puts JSON.pretty_generate(@@full_stats)
  f.close

end

#too_many_errors_received ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 164

def too_many_errors_received
  $LOG.error "Too many errors: #{@@error_count} errors on #{@@count} executed sequences, exiting before finishing"
end

#trash_checkpointed_work ⇒ Object

read a work that will not be processed, only to skip until checkpoint



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 202

def trash_checkpointed_work

  @@chunk_size.times do
    begin
      n,f,q,c = @@fqr.next_seq
    end while (!n.nil? && @@params.repeated_seq?(n))

    if n.nil?
      break
    end
  end

end

#work_received(obj) ⇒ Object

def next_work

  if @@exit
    return nil
  end
  group = SequenceGroup.new

  @@chunk_size.times do
    begin

      n,f,q,c = @@fqr.next_seq

      if !n.nil? && @@params.repeated_seq?(n)
        @@full_stats.add_stats({'sequences' => {'count' => {'rejected' => 1}}})
        @@full_stats.add_stats({'sequences' => {'rejected' => {'repeated' => 1}}})

        get_file(File.join(OUTPUT_PATH,'rejected.txt')).puts('>'+n+ ' repeated')

      end
      if !n.nil?
        @@full_stats.add_stats({'sequences' => {'count' => {'input_count' => 1}}})
      end
    end while (!n.nil? && @@params.repeated_seq?(n))

    if !n.nil?
      # @@full_stats.add_stats({'sequences' => {'count' => {'processed' => 1}}})
      group.push SequenceWithAction.new(n,f.upcase,q,c)
    else
      break
    end
  end

  # puts "Processing #{group.inspect}"

  if group.empty?
    return nil
  else
    return group
  end

end



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 290

def work_received(obj)

  res = obj

  # collect stats
  @@full_stats.add_stats(obj.stats)

  # print output in screen
  puts obj.output_text

  # save results to files
  save_files(obj)

end

#worker_initial_config ⇒ Object 



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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 168

def worker_initial_config
  return @@params
end