Class: CagnutToolbox::QseqToFastq

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/cagnut_toolbox/functions/qseq_to_fastq.rb

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ QseqToFastq

Returns a new instance of QseqToFastq.



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# File 'lib/cagnut_toolbox/functions/qseq_to_fastq.rb', line 9

def initialize opts = {}
  @order = sprintf '%02i', opts[:order]
  @input = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
  @input.gsub! '.gz', ''
  @input2 = File.expand_path fetch_filename, File.dirname(@input)
  abort('Cant recognized sequence files') if @input2.nil?
  @output = "#{opts[:dirs][output]}/#{sample_name}_1_qtf.fastq"
  @output2 = "#{opts[:dirs][output]}/s_#{sample_name}_2_qtf.fastq"
  @job_name = "#{prefix_name}_qseq_to_fastq_#{sample_name}"
end

Instance Method Details

#fetch_filename ⇒ Object 



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# File 'lib/cagnut_toolbox/functions/qseq_to_fastq.rb', line 20

def fetch_filename
  filename = File.basename(@input)
  if filename.match '_R1_'
    filename.gsub '_R1_', '_R2_'
  elsif filename.match '_1_'
    filename.gsub '_1_', '_2_'
  end
end

#generate_script ⇒ Object 



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# File 'lib/cagnut_toolbox/functions/qseq_to_fastq.rb', line 43

def generate_script
  script_name = "#{@order}_toolbox_qseq2fastq"
  exe_qseq_to_fastq = "ruby #{exe_path}/qseq_to_fastq.rb"
  file = File.join jobs_dir, "#{script_name}.sh"
  File.open(file, 'w') do |f|
    f.puts <<-BASH.strip_heredoc
      #!/bin/bash

      cd "#{jobs_dir}/../"
      echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
      if [ -s "#{@input}.gz" ]
      then
        gunzip -c #{@input}.gz | #{exe_qseq_to_fastq} #{@output} \\
          #{::Cagnut::JobManage.run_local}
        gunzip -c #{@input2}.gz | #{exe_qseq_to_fastq} #{@output2} \\
          #{::Cagnut::JobManage.run_local}
      else
        cat #{@input} | #{exe_qseq_to_fastq} #{@output} \\
          #{::Cagnut::JobManage.run_local}
        cat #{@input2} | #{exe_qseq_to_fastq} #{@output2} \\
          #{::Cagnut::JobManage.run_local}
      fi

      #force error when missing/empty fastq . Would prevent continutation of pipeline
      if [ ! -s "#{@output2}" ]
      then
        echo "Missing FASTQ: #{@output2} file!"
        exit 100
      fi
      echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"

    BASH
  end
  File.chmod(0700, file)
end

#queuing_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_toolbox/functions/qseq_to_fastq.rb', line 36

def queuing_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    tools: ['toolbox', 'qseq_to_fastq']
  }
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_toolbox/functions/qseq_to_fastq.rb', line 29

def run previous_job_id = nil
  puts "Submitting #{sample_name} qseqToFastq"
  script_name = generate_script task
  ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
  [@job_name, @output]
end