Module: CustomDS

Defined in:
lib/MARQ/CustomDS.rb

Constant Summary collapse

@@r = 
nil

Class Method Summary collapse

Class Method Details

.clean(dataset) ⇒ Object 



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# File 'lib/MARQ/CustomDS.rb', line 53

def self.clean(dataset)
  dataset.sub(/_cross_platform/,'')
end

.customdir ⇒ Object 



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# File 'lib/MARQ/CustomDS.rb', line 7

def self.customdir
  File.join(MARQ.datadir,'CustomDS')
end

.datasets(org) ⇒ Object 



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# File 'lib/MARQ/CustomDS.rb', line 61

def self.datasets(org)
  Dir.glob(File.join(customdir, org) + '/*.orders').collect{|f| clean(File.basename(f.sub(/.orders/,'')))}.uniq
end

.has_cross_platform?(dataset) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/MARQ/CustomDS.rb', line 57

def self.has_cross_platform?(dataset)
  Dir.glob(path(clean(dataset)) + '_cross_platform.orders').any?
end

.info(dataset) ⇒ Object 



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# File 'lib/MARQ/CustomDS.rb', line 20

def self.info(dataset)
  begin
    text =  Open.read(path(dataset) + '.description')
    if text =~ /(.*)\n--\n(.*)/
      {:title => $1.strip, :description => $2.strip}
    elsif text.collect.length > 1 || text.length > 200
      {:title => "", :description => text}
    else
      {:title => text, :description => ""}
    end
  rescue Exception
    puts $!.message
    {:title => "" , :description => "" }
  end
end

.is_cross_platform?(dataset) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/MARQ/CustomDS.rb', line 49

def self.is_cross_platform?(dataset)
  dataset.match(/_cross_platform/)
end

.organism(dataset) ⇒ Object 



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# File 'lib/MARQ/CustomDS.rb', line 45

def self.organism(dataset)
  path(dataset).match(/#{ customdir }\/(.*?)\//)[1]
end

.path(dataset) ⇒ Object 



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# File 'lib/MARQ/CustomDS.rb', line 36

def self.path(dataset)
  files = Dir.glob(customdir + "/*/#{ dataset }.orders")
  if files.length == 1
    files.first.sub(/.orders/,'')
  else
    Dir.glob(customdir + "/*/#{ dataset }").first
  end
end

.process(name) ⇒ Object 



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# File 'lib/MARQ/CustomDS.rb', line 65

def self.process(name)
  puts "Processing #{ name }"
  org = organism(name)
  prefix = File.join(customdir, org, name)
  conditions = Dir.glob(prefix + '/*').collect{|f| File.basename(f)} - %w(values codes info description cross_platform)
  description = Open.read(File.join(prefix, 'description'))

  info = YAML.load(File.open(File.join(prefix, 'info')))
  r.CustomDS_process(prefix, false, conditions, description, info["two_channel"], !info["log2"])


  codes = Open.read(File.join(prefix,'codes')).collect{|l| l.chomp}
  cross_platform = ID.translate(org, codes) 

  if cross_platform.length > codes.length / 4
    Open.write(File.join(prefix,'cross_platform'),cross_platform.collect{|c| c || "NO MATCH"}.join("\n"))
    r.CustomDS_process(prefix, true, conditions, description, info["two_channel"], !info["log2"])
  end
end

.r ⇒ Object 



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# File 'lib/MARQ/CustomDS.rb', line 11

def self.r
  if @@r.nil?
    RSRuby.instance.source(MARQ.rootdir + '/R/MA.R')
    RSRuby.instance.source(MARQ.rootdir + '/R/CustomDS.R')
    @@r = RSRuby.instance
  end
  @@r
end