Class: Experiment

Inherits:
Object
  • Object
show all
Defined in:
lib/experiment.rb

Instance Method Summary collapse

Constructor Details

#initialize(name, basedir) ⇒ Experiment

Returns a new instance of Experiment.



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# File 'lib/experiment.rb', line 7

def initialize(name, basedir)
  @name = name
  @base_dir = basedir
end

Instance Method Details

#dirname(a) ⇒ Object 



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# File 'lib/experiment.rb', line 11

def dirname(a)
  File.join @base_dir, 'experiments', @name, a
end

#expand_with_updates(opts, updates_are_full_alignments = true) ⇒ Object 



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# File 'lib/experiment.rb', line 30

def expand_with_updates(opts, updates_are_full_alignments = true)
  ali = self.dirname("alignment")
  phy = opts[:phylip]
  raise "phylip file not available" if phy.nil? or not File.exist?(phy)
  FileUtils.copy phy, ali 
  p = Phylip.new(File.join ali, File.basename(phy))
  p.subdivide_random opts 
end

#last_bunch_dir ⇒ Object 



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# File 'lib/experiment.rb', line 14

def last_bunch_dir
  dirs = Dir.entries(dirname("output")).select{|f| f =~ /^bunch/}
  dirs.sort_by{|s| s.split("_").last.to_i}.last
end

#setup_dirs ⇒ Object 



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# File 'lib/experiment.rb', line 18

def setup_dirs
  setup_ready = true
  %w(alignment output).map{|n| self.dirname n}.each do |dir|
    if File.exist?(dir)
      puts "Exists #{dir}"
      setup_ready = false # to avoid overwrite
    else
      FileUtils.mkdir_p dir
    end
  end
  setup_ready
end