Class: CagnutSnpeff::SnpAnnotation

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ SnpAnnotation

Returns a new instance of SnpAnnotation.



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# File 'lib/cagnut_snpeff/functions/snp_annotation.rb', line 9

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

Instance Method Details

#annotation_options ⇒ Object 



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# File 'lib/cagnut_snpeff/functions/snp_annotation.rb', line 31

def annotation_options
  array = annotation_params['params'].dup
  array << "#{@input} > #{@output}"
  array.uniq
end

#cluster_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_snpeff/functions/snp_annotation.rb', line 23

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

#generate_script ⇒ Object 



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# File 'lib/cagnut_snpeff/functions/snp_annotation.rb', line 49

def generate_script
  script_name = "#{@order}_snpeff_snp_annotation"
  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"

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

      EXITSTATUS=$?

      #force error when missing output
      if [ ! -s "#{@output}" ]; then exit 100;fi;
      if [ $(grep -cv "^#" "#{@output}") -eq "0" ]
      then
        echo "No variants!"
        exit 100;
      fi

      if [ $EXITSTATUS -eq 1 ];then
        echo "Error in Java"
        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

#modified_java_array ⇒ Object 



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# File 'lib/cagnut_snpeff/functions/snp_annotation.rb', line 37

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

#params_combination_hash ⇒ Object 



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# File 'lib/cagnut_snpeff/functions/snp_annotation.rb', line 42

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

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_snpeff/functions/snp_annotation.rb', line 16

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