class CagnutBwa::Aln

Public Class Methods

new(opts = {}) click to toggle source
# 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

Public Instance Methods

aln_params_for_r1() click to toggle source
# 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() click to toggle source
# 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() click to toggle source
# 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() click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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