Module: MARQ::Dataset

Defined in:
lib/MARQ/main.rb

Class Method Summary collapse

Class Method Details

.broken?(dataset) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/MARQ/main.rb', line 121

def self.broken?(dataset)
  path = path(dataset)

  return false if path.nil?
  
  if File.exists?(path + '.skip')
    return true
  else
    return false
  end
end

.codes(dataset) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 214

def self.codes(dataset)
  read_file(dataset, 'codes').split(/\n/)
end

.codes_for(dataset, type, experiment) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 234

def self.codes_for(dataset, type, experiment)
  codes  = codes(dataset)
  values = send(type, dataset)[experiment]
  Hash[*codes.zip(values).reject{|p| p.last.nil? }.flatten]
end

.exists?(dataset) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/MARQ/main.rb', line 112

def self.exists?(dataset)
  path = path(dataset)
  if path.nil?
    return false
  else
    return File.exists?(path + '.orders')
  end
end

.experiments(dataset) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 210

def self.experiments(dataset)
  read_file(dataset, 'experiments').split(/\n/).collect{|exp| exp.strip }
end

.has_cross_platform?(dataset) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/MARQ/main.rb', line 137

def self.has_cross_platform?(dataset)
  File.exists?(path(dataset) + '_cross_platform.orders')
end

.info(name) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 141

def self.info(name)
  begin
    title, description = Open.read(path(name) + '.description').split(/\n--\n/).values_at(0,1)
    {:title => title.strip, :description => description.strip}
  rescue Exception
    puts $!.message
    {:title => "" , :description => "" }
  end
end

.is_cross_platform?(dataset) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/MARQ/main.rb', line 133

def self.is_cross_platform?(dataset)
  MARQ::Name.is_cross_platform? dataset
end

.is_GEO?(dataset) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/MARQ/main.rb', line 100

def self.is_GEO?(dataset)
  ! dataset.match(/^(?:GDS|GSE)/).nil?
end

.logratios(dataset) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 222

def self.logratios(dataset)
  read_values(dataset, 'logratios')
end

.orders(dataset) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 218

def self.orders(dataset)
  read_values(dataset, 'orders', true)
end

.organism(dataset) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 159

def self.organism(dataset)
  MARQ::Platform.organism(platform(dataset))
end

.path(platform) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 104

def self.path(platform)
  if is_GEO? platform
    GEO.dataset_path(platform)
  else
    CustomDS.dataset_path(platform)
  end
end

.platform(dataset) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 151

def self.platform(dataset)
  if is_GEO? dataset
    GEO.dataset_platform(dataset)
  else
    CustomDS.dataset_platform(dataset)
  end
end

.process(dataset, platform = nil) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 163

def self.process(dataset, platform = nil)
  if is_GEO? dataset
    GEO.process_dataset(dataset, platform)
  else
    CustomDS.process_dataset(dataset, platform)
  end
end

.pvalues(dataset) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 226

def self.pvalues(dataset)
  read_values_t(dataset, 'pvalues')
end

.read_file(dataset, ext) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 171

def self.read_file(dataset, ext)
  Open.read(path(dataset) + '.' + ext)
end

.read_values(dataset, file, integer = false) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 175

def self.read_values(dataset, file, integer = false)
  result = {}

  experiments = experiments(dataset)
  experiments.each{|experiment| result[experiment] = [] }
  read_file(dataset, file).split(/\n/).each do |line|
    values = line.chomp.split(/\t/)
    if integer
      values.each_with_index{|value, i| result[experiments[i]] << (value == 'NA' ? nil : value.to_i)}
    else
      values.each_with_index{|value, i| result[experiments[i]] << (value == 'NA' ? nil : value.to_f)}
    end
  end

  result
end

.read_values_t(dataset, file) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 192

def self.read_values_t(dataset, file)
  experiments = experiments(dataset).reject{|experiment| MARQ::Name.is_ratio? experiment }
 
  return {} if experiments.empty?

  result = {}

  experiments.each{|experiment| result[experiment] = [] }

  read_file(dataset, file).split(/\n/).each do |line|
    values = line.chomp.split(/\t/)
    values.each_with_index{|value, i| result[experiments[i]] << (value == 'NA' ? nil : value.to_f) }
  end

  result
end

.t(dataset) ⇒ Object 



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# File 'lib/MARQ/main.rb', line 230

def self.t(dataset)
  read_values_t(dataset, 't')
end