Module: MADB::CustomDS

Defined in:
lib/MARQ/MADB.rb

Class Method Summary collapse

Class Method Details

.platform_entries(platform) ⇒ Object 



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# File 'lib/MARQ/MADB.rb', line 107

def self.platform_entries(platform)
  DBcache.num_rows(platform)
end

.positions(dataset, genes) ⇒ Object 



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

def self.positions(dataset, genes)
  return [{},[]] if genes.empty?
  genes = genes.collect{|gene| gene.downcase.strip}

  platform_entries = platform_entries(dataset + '_codes').to_f

  data = {}
  matched = []

  gene_positions = DBcache.load(dataset, genes)
  matched ||= gene_positions.keys

  experiments = DBcache.load(dataset + '_experiments').sort{|a,b| 
    a[0].to_i <=> b[0].to_i
  }.collect{|p| 
    Object::GEO::clean(dataset) + ": " + p[1].first
  }


  matched = (matched + gene_positions.keys).uniq
  scale = (0..experiments.length - 1).collect{|i| 
    rows = DBcache.num_rows(dataset, "C#{i}"); 
    if rows > 0 
      platform_entries / rows 
    else 
      nil 
    end 
  }

  gene_x_experiment = gene_positions.values

  experiment_x_gene = gene_x_experiment.transpose

  experiments.each_with_index{|experiment, i|
    next if scale[i].nil? || experiment_x_gene[i].nil?
    values = experiment_x_gene[i].collect{|v| v.nil? ? nil : (v.to_f * scale[i]).to_i}
    data[experiment] = values
  }
  
  [data, matched]
end

.save(dataset) ⇒ Object 



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# File 'lib/MARQ/MADB.rb', line 8

def self.save(dataset)
  prefix = Object::CustomDS.path(dataset)

  codes = File.open(prefix  + '.codes').collect{|l| l.chomp.downcase}
  
  DBcache.save(dataset + '_codes', codes)

  experiments = File.open(prefix + '.experiments').collect{|l| l.chomp}
  orders = File.open(prefix + '.orders').collect{|l| values = l.chomp.split(/\t/).collect{|v| v == "NA" ? nil : v.to_i };}

  data = {}
  codes.each_with_index{|code,i|
    data[code.to_sym] = orders[i]
  }
  case 
  when codes.length < 65535
    type = "SMALLINT UNSIGNED"
  when codes.length < 16777215
    type = "MEDIUMIN UNSIGNED"
  else
    type = "INT UNSIGNED"
  end

  puts "Saving #{ dataset }"
  DBcache.save(dataset + '_experiments', experiments)
  DBcache.save(dataset, data, [type] * orders.first.length)

  return unless Object::CustomDS::has_cross_platform?(dataset)
  dataset = dataset + '_cross_platform'
  prefix = Object::CustomDS.path(dataset)

  codes = File.open(prefix  + '.codes').collect{|l| l.chomp.downcase}
  
  DBcache.save(dataset + '_codes', codes)

  experiments = File.open(prefix + '.experiments').collect{|l| l.chomp}
  orders = File.open(prefix + '.orders').collect{|l| values = l.chomp.split(/\t/).collect{|v| v == "NA" ? nil : v.to_i };}

  data = {}
  codes.each_with_index{|code,i|
    data[code.to_sym] = orders[i]
  }
  case 
  when codes.length < 65535
    type = "SMALLINT UNSIGNED"
  when codes.length < 16777215
    type = "MEDIUMIN UNSIGNED"
  else
    type = "INT UNSIGNED"
  end

  puts "Saving #{ dataset }"
  DBcache.save(dataset + '_experiments', experiments)
  DBcache.save(dataset, data, [type] * orders.first.length)
  nil
end