Module: Ms::Quant::Cmdline

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

Class Method Summary collapse

Class Method Details

.args_to_hashes(args, replicate_postfix = "-rep") ⇒ Object

expects arguments in one of two forms. The first form is grouped by condition as shown:

condition1=file1,file2,file3... condition2=file4,file5...

The second is where each file is its own condition (1 replicate):

file1 file2 file3

Returns three ordered hashes (only ordered for ruby 1.9): 

1) Condition to an array of samplenames
2) Samplename to the filename  
3) Samplename to condition



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# File 'lib/ms/quant/cmdline.rb', line 21

def self.args_to_hashes(args, replicate_postfix="-rep")
  # groupname => files
  condition_to_samplenames = {}
  samplename_to_filename = {}
  args.each do |arg|
    (condition, files) = 
      if arg.include?('=')
        (condition, filestring) = arg.split('=')
        [condition, filestring.split(',')]
      else
        [basename(arg), [arg]]
      end
    sample_to_file_pairs = files.each_with_index.map do |file,i| 
      rep_string = (files.size == 1) ? "" : "#{replicate_postfix}#{i+1}"
      ["#{condition}#{rep_string}", file] 
    end
    sample_to_file_pairs.each {|name,file| samplename_to_filename[name] = file }
    condition_to_samplenames[condition] = sample_to_file_pairs.map(&:first)
  end
  [samplename_to_filename, condition_to_samplenames, condition_to_samplenames.inverse]
end