SCBI_MapReduce, a New Ruby Task-Farm Skeleton for Automated Parallelisation and Distribution in Chunks of Sequences: The Implementation of a Boosted Blast+

Algorithm 1

class MyWorkerManager < WorkManager

  def self.init_work_manager

 # open input fastq file, and results as output

 @@fastq_file=FastqFile.new(fastq_file_path)

 @@results=FastqFile.new( ‘ ./results.fastq ’ , ‘ w+ ’ )

  end

  def self.end_work_manager

 #close files on finish

 @@fastq_file.close

 @@results.close

  end

  # this method is called every time a worker

  # needs a new work

  def next_work

 # get next sequence or nil from file

 name,fasta,qual,comments=@@fastq_file.next_seq

 if !name.nil?

   return name,fasta,qual,comments

 else

   return nil

 end

  end

  def work_received(results)

 # write results to disk

 results.each do ∣name,fasta,qual,comments∣

   @@results.write_seq(name,fasta,qual,comments)

 end

  end

end