Class: Xcalibur::Convert::RawToMgf

Inherits:
Tap::Workflow
  • Object
show all
Defined in:
lib/xcalibur/convert/raw_to_mgf.rb

Overview

:startdoc::manifest convert RAW files to mgf format Extracts spectra from a .RAW file and formats them as mgf (Mascot Generic Format). RawToMgf is a workflow that uses the RawToDta and DtaToMgf tasks, and can be configured through these tasks using the following configuration files:

config/xcalibur/convert
|- raw_to_mgf.yml               # configures RawToMgf
`- raw_to_mgf
 |- raw_to_dta.yml              # configures RawToDta
 `- dta_to_mgf.yml              # configures DtaToMgf

Mgf files are named after the RAW file they represent; the group merge file is named ‘merge.mgf’ although an alternate merge file name can be specified in the options.

Instance Method Summary collapse

Instance Method Details

#workflow ⇒ Object 



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# File 'lib/xcalibur/convert/raw_to_mgf.rb', line 29

def workflow 
  # Define the workflow entry and exit points,
  # as well as the workflow logic.
  
  raw_to_dta = Xcalibur::Convert::RawToDta.new
  dta_to_mgf = Xcalibur::Convert::DtaToMgf.new
  
  dta_dirs = []
  n_inputs = nil
  self.entry_point = Tap::Task.new do |task, *input_files|
    n_inputs = input_files.length
    input_files.each do |input_file|
      dta_dir = File.basename(input_file).chomp(File.extname(input_file))
      dta_dirs << dta_dir
      raw_to_dta.enq(input_file, dta_dir)
    end
  end
  
  group_results = []
  raw_to_dta.on_complete do |_result|
    if merge_individual
      input_file = _result._original[0]
      output_file = File.join( File.dirname(merge_file), File.basename(input_file).chomp(File.extname(input_file)) + ".mgf")
      dta_to_mgf.enq(output_file, *_result._expand)
    end
    
    # collect _results to determine when all the input
    # files have been processed by raw_to_dta
    group_results << _result
    
    # When all the input files have been converted, merge the
    # group and enque a task to cleanup the dta files, as specified.
    if group_results.length == n_inputs
      if merge_group
        all_results = group_results.collect {|_result| _result._expand }.flatten
        dta_to_mgf.enq(merge_file, *all_results)
      end
      
      if remove_dta_files
        cleanup = Tap::Task.new do |task, raw_dir|           
          task.log :rm, raw_dir
          
          # take this stepwise to be a little safer...
          FileUtils.rm Dir.glob(raw_dir + "/*.dta")
          FileUtils.rm ["#{raw_dir }/lcq_dta.txt", "#{raw_dir }/lcq_profile.txt"]
          FileUtils.rmdir raw_dir
        end
        dta_dirs.each {|dir| cleanup.enq(dir)}
      end
    end
  end

  self.exit_point = dta_to_mgf
end