Module: MADB

Defined in:
lib/MARQ/MADB.rb

Class Method Summary collapse

Class Method Details

.load_positions(dataset, genes) ⇒ Object 



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# File 'lib/MARQ/MADB.rb', line 85

def self.load_positions(dataset, genes)
  positions   = DBcache.load(dataset, genes)
  experiments = 
    DBcache.load(dataset + '_experiments').
      sort_by {|p| p[0].to_i }.
      collect {|p| MARQ::Name.clean(dataset) + ": " + p[1].first }


  
  result = {}; experiments.each {|exp| result[exp] = [] }
  positions.values_at(*genes).each do |values|
    experiments.zip(values || []).each do |p|
      experiment, value = p
      result[experiment] << (value.nil? ? nil : value.to_i)
    end
  end

  result
end

.num_codes(dataset) ⇒ Object 



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# File 'lib/MARQ/MADB.rb', line 81

def self.num_codes(dataset)
  DBcache.num_rows(dataset + '_codes')
end

.num_values(dataset) ⇒ Object

{{{ Loading Positions



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# File 'lib/MARQ/MADB.rb', line 69

def self.num_values(dataset)
  experiments = 
    DBcache.load(dataset + '_experiments').
      sort_by {|p| p[0].to_i }.
      collect {|p| MARQ::Name.clean(dataset) + ": " + p[1].first }

  values = {}
  experiments.each_with_index do |exp, i| values[exp] = DBcache.num_rows(dataset, "C#{i}") end

  values
end

.save_dataset(dataset) ⇒ Object

Save dataset, all instances, cross_platform if available.



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# File 'lib/MARQ/MADB.rb', line 42

def self.save_dataset(dataset)
  save_dataset_instance(dataset)
  save_dataset_instance(MARQ::Name.cross_platform(dataset)) if MARQ::Dataset.has_cross_platform?(dataset)
  nil
end

.save_dataset_instance(dataset) ⇒ Object

Save the actual data, cross_platform or not



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

def self.save_dataset_instance(dataset)

  # Get info
  codes        = MARQ::Dataset.codes(dataset);
  experiments  = MARQ::Dataset.experiments(dataset);
  orders       = MARQ::Dataset.orders(dataset).values_at(*experiments).transpose;

  # Save codes and experiments
  DBcache.save(dataset + '_codes', codes)
  DBcache.save(dataset + '_experiments', experiments)

  # Asign orders to codes
  data = {}
  codes.each_with_index{|code,i|
    data[code] = orders[i]
  }

  # Save orders
  case 
  when codes.length < 65535
    type = "SMALLINT UNSIGNED"
  when codes.length < 16777215
    type = "MEDIUMINT UNSIGNED"
  else
    type = "INT UNSIGNED"
  end
  DBcache.save(dataset, data, [type] * orders.first.length)

end

.save_platform(platform) ⇒ Object 



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# File 'lib/MARQ/MADB.rb', line 55

def self.save_platform(platform)
  datasets = MARQ::Platform.datasets(platform).sort
  return if datasets.empty?

  save_platform_instance(platform)
  save_platform_instance(MARQ::Name.cross_platform(platform)) if MARQ::Platform.has_cross_platform?(platform)
  
  datasets.sort.each do |dataset|
    save_dataset(dataset)
  end
end

.save_platform_instance(platform) ⇒ Object 



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# File 'lib/MARQ/MADB.rb', line 48

def self.save_platform_instance(platform)
  DBcache.save(platform + '_codes', 
               MARQ::Platform.is_cross_platform?(platform) ? 
                 MARQ::Platform.cross_platform(platform) : 
                 MARQ::Platform.codes(platform))
end