Class: CagnutBwa::Aln

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ Aln

Returns a new instance of Aln.



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# File 'lib/cagnut_bwa/functions/aln.rb', line 8

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

Instance Method Details

#aln_params_for_r1 ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln.rb', line 45

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

#aln_params_for_r2 ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln.rb', line 54

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

#fetch_filename ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln.rb', line 18

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_bwa/functions/aln.rb', line 63

def generate_script
  script_name = "#{@order}_bwa_aln"
  file = File.join jobs_dir, "#{script_name}.sh"
  template = Tilt.new(File.expand_path '../templates/aln.sh', __FILE__)
  File.open(file, 'w') do |f|
    f.puts template.render Object.new, job_params(script_name)
  end
  File.chmod(0700, file)
  script_name
end

#job_params(script_name) ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln.rb', line 74

def job_params script_name
  {
    jobs_dir: jobs_dir,
    script_name: script_name,
    input: @input,
    input2: @input2,
    output: @output,
    output2: @output2,
    aln_params_for_r1: aln_params_for_r1,
    aln_params_for_r2: aln_params_for_r2,
    run_local: ::Cagnut::JobManage.run_local
  }
end

#queuing_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln.rb', line 34

def queuing_options previous_job_id = nil
  threads = 2
  {
    previous_job_id: previous_job_id,
    var_env: [ref_fasta],
    adjust_memory: ["h_vmem=adjustWorkingMem 5G #{threads}"],
    parallel_env: [threads],
    tools: ['bwa', 'aln']
  }
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/functions/aln.rb', line 27

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