Module: MADB::GEO

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 229

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

.positions(platform, genes) ⇒ Object 



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# File 'lib/MARQ/MADB.rb', line 185

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

  datasets = Object::GEO.platform_datasets(platform).sort
  platform_entries = platform_entries(platform).to_f

  data = {}
  matched = nil

  datasets.each{|dataset|
    dataset += '_cross_platform' if Object::GEO::is_cross_platform?(platform)
    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
    }

    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

.saveGPL(platform) ⇒ Object 



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# File 'lib/MARQ/MADB.rb', line 119

def self.saveGPL(platform)
  datasets = Object::GEO.platform_datasets(platform).sort
  return if datasets.empty?

  puts "Saving #{ platform }, #{datasets.length} datasets"

  codes = File.open(File.join(Object::GEO.platform_path(platform),'codes')).collect{|l| l.chomp.downcase}
  
  DBcache.save(platform, codes)

  Progress.monitor("Saving #{ platform }")
  datasets.sort.each{|dataset|
    path = Object::GEO.dataset_path(dataset)
    experiments = File.open(path + '.experiments').collect{|l| l.chomp}
    orders = File.open(path + '.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 = "MEDIUMINT UNSIGNED"
    else
      type = "INT UNSIGNED"
    end

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


  return unless File.exist?(File.join(Object::GEO.platform_path(platform),'cross_platform'))
  codes = File.open(File.join(Object::GEO.platform_path(platform),'cross_platform')).collect{|l| l.chomp.downcase}

  DBcache.save(platform + '_cross_platform', codes)

  Progress.monitor("Saving #{ platform }")
  datasets.sort.each{|dataset|
    path = Object::GEO.dataset_path(dataset)
    next unless File.exists?(path + '_cross_platform.experiments')
    experiments = File.open(path + '_cross_platform.experiments').collect{|l| l.chomp}
    orders = File.open(path + '_cross_platform.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


    DBcache.save(dataset + '_cross_platform_experiments', experiments)
    DBcache.save(dataset + '_cross_platform', data, [type] * orders.first.length)
  }
end