Method: Ms::Quant::Qspec#run

Defined in:
lib/ms/quant/qspec.rb

#run(normalize = true, opts = {}) ⇒ Object

returns an array of Qspec::Results objects (each object can be considered a row of data)



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# File 'lib/ms/quant/qspec.rb', line 79

def run(normalize=true, opts={})
  puts "normalize: #{normalize}" if $VERBOSE
  tfile = Tempfile.new("qspec")
  write(tfile.path)
  if opts[:keep]
    local_file = File.join(Dir.pwd,File.basename(tfile.path))
    FileUtils.cp(tfile.path, local_file, :verbose => $VERBOSE)
    puts "(copy of) file submitted to qspec: #{local_file}" if $VERBOSE
  end
  qspec_exe = self.class.executable(conditions)
  cmd = [qspec_exe, tfile.path, NBURNIN, NITER, (normalize ? 1 : 0)].join(' ')
  if $VERBOSE
    puts "running #{cmd}" if $VERBOSE
  else
    cmd << " 2>&1"
  end
  reply = `#{cmd}`
  puts reply if $VERBOSE
  outfile = tfile.path + '_' + qspec_exe
  results = self.class.results_array(outfile)
  if opts[:keep]
    local_outfile = File.join(Dir.pwd, File.basename(outfile))
    FileUtils.cp(outfile, local_outfile, :verbose => $VERBOSE)
    puts "(copy of) file returned from qspec: #{outfile}"
  end
  tfile.unlink
  results
end