Class: CagnutGatk::VariantEval

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ VariantEval

Returns a new instance of VariantEval.



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# File 'lib/cagnut_gatk/functions/variant_eval.rb', line 9

def initialize opts = {}
  @order = sprintf '%02i', opts[:order]
  @vcf_dir = opts[:dirs][:output]
  @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_filtered.vcf" : opts[:input]
  @output = "#{@vcf_dir}/#{sample_name}.eval"
  @job_name = "#{prefix_name}_snpEval_#{sample_name}"
end

Instance Method Details

#cluster_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_gatk/functions/variant_eval.rb', line 25

def cluster_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    adjust_memory: ['h_stack=256M', 'h_vmem=8G'],
    tools: ['gatk', 'variant_eval']
  }
end

#generate_script ⇒ Object 



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# File 'lib/cagnut_gatk/functions/variant_eval.rb', line 56

def generate_script
  script_name = "#{@order}_gatk_variant_eval"
  file = File.join jobs_dir, "#{script_name}.sh"
  ltag = target.nil? ? '' : "-L #{target}"
  File.open(file, 'w') do |f|
    f.puts <<-BASH.strip_heredoc
      #!/bin/bash

      cd "#{jobs_dir}/../"
      echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
      EVALNAME=$(basename #{@vcf_dir}/#{sample_name})

      #{params_combination['java'].join("\s")} \\
        #{params_combination['params'].join(" \\\n            ")} \\
        #{::Cagnut::JobManage.run_local}

      EXITSTATUS=$?

      if [ ! -s "#{@output}" ]
      then
        echo "Missing #{@output}"
        exit 100
      fi
      echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"

      exit $EXITSTATUS
    BASH
  end
  File.chmod(0700, file)
  script_name
end

#modified_java_array ⇒ Object 



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# File 'lib/cagnut_gatk/functions/variant_eval.rb', line 44

def modified_java_array
  array = variant_eval_params['java'].dup
  array.unshift(java_path).uniq
end

#params_combination ⇒ Object 



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# File 'lib/cagnut_gatk/functions/variant_eval.rb', line 49

def params_combination
  @params_combination_hash ||= {
    'java' => modified_java_array,
    'params' => variant_eval_options
  }
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_gatk/functions/variant_eval.rb', line 17

def run previous_job_id = nil
  return unless snpdb
  puts "Submitting #{sample_name} Jobs: variant (SNPs, INDELs) -evaluation "
  script_name = generate_script
  ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
  @job_name
end

#variant_eval_options ⇒ Object 



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# File 'lib/cagnut_gatk/functions/variant_eval.rb', line 33

def variant_eval_options
  array = variant_eval_params['params'].dup
  array << "-T VariantEval"
  array << "-R #{ref_fasta}"
  array << "--dbsnp #{snpdb}"
  array << "-o #{@output}"
  array << "--eval:$EVALNAME #{@input}"
  array << "-L #{target}" if target
  array.uniq
end