Class: CagnutBwa::AlnOneFastq

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ AlnOneFastq

Returns a new instance of AlnOneFastq.



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# File 'lib/cagnut_bwa/functions/aln_one_fastq.rb', line 9

def initialize opts = {}
  @order = sprintf '%02i', opts[:order]
  @input = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
  abort('Cant recognized sequence files') if @input.nil?
  @input2 = File.expand_path fetch_filename(@input), File.dirname(@input) if @input.match '_1_'
  @output = "#{opts[:dirs][:output]}/#{File.basename(@input).gsub('.gz', '').gsub('.txt','.sai')}"
  @output2 = "#{opts[:dirs][:output]}/#{fetch_filename(@output)}" if @input.match '_1_'
  @job_name = "#{prefix_name}_#{sample_name}_Aln_one_fastq"
end

Instance Method Details

#aln_params_for_r1 ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln_one_fastq.rb', line 46

def aln_params_for_r1
  array = aln_params.dup
  array.insert 1, 'aln'
  array << "#{ref_fasta}"
  array << "-f #{@output}"
  array << "#{@input}"
  array.uniq
end

#aln_params_for_r2 ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln_one_fastq.rb', line 55

def aln_params_for_r2
  array = aln_params.dup
  array.insert 1, 'aln'
  array << "#{ref_fasta}"
  array << "-f #{@output2}"
  array << "#{@input2}"
  array.uniq
end

#fetch_filename(file) ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln_one_fastq.rb', line 19

def fetch_filename file
  filename = File.basename(file)
  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_bwa/functions/aln_one_fastq.rb', line 64

def generate_script
  script_name = "#{@order}_bwa_aln_one_fastq"
  file = File.join jobs_dir, "#{script_name}.sh"
  File.open(file, 'w') do |f|
    f.puts <<-BASH.strip_heredoc
      #!/bin/bash
      echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
      if [[ #{@input} =~ _1_ ]]
      then
        #{aln_params_for_r2.join(" \\\n            ")} \\
          #{::Cagnut::JobManage.run_local}
      else
      fi

      #{aln_params_for_r1.join(" \\\n            ")} \\
        #{::Cagnut::JobManage.run_local}

      if [ ! -s "#{@output}" ]
      then
        echo "Missing SAI:#{@output} 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)
  script_name
end

#queuing_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln_one_fastq.rb', line 35

def queuing_options previous_job_id = nil
  threads = 2
  {
    previous_job_id: previous_job_id,
    var_env: [fastq_dir, sai_dir, threads],
    adjust_memory: ['h_vmem=3.4G'],
    parallel_env: [threads],
    tools: ['bwa', 'aln']
  }
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln_one_fastq.rb', line 28

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