Method: BioMart.query

Defined in:
lib/rbbt/sources/biomart.rb

.query(database, main, attrs = nil, filters = nil, data = nil, open_options = {}) ⇒ Object

This method performs a query in biomart for a datasets and a given set of attributes, there must be a main attribute that will be used as the key in the result hash, optionally there may be a list of additional attributes and filters. The data parameter at the end is used internally to incrementally building the result, due to a limitation of the BioMart WS that only allows 3 external arguments, users normally should leave it unspecified or nil. The result is a hash, where the keys are the different values for the main attribute, and the value is a hash with every other attribute as key, and as value and array with all possible values (Note that for a given value of the main attribute, there may be more than one value for another attribute). If filters is left a nil it adds a filter to the BioMart query to remove results with the main attribute empty, this may cause an error if the BioMart WS does not allow filtering with that attribute.



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# File 'lib/rbbt/sources/biomart.rb', line 136

def self.query(database, main, attrs = nil, filters = nil, data = nil, open_options = {})
  open_options = Misc.add_defaults open_options, :nocache => false, :filename => nil, :field_names => nil, :by_chr => false
  filename, field_names, by_chr = Misc.process_options open_options, :filename, :field_names, :by_chr
  attrs   ||= []
  open_options = Misc.add_defaults open_options, :keep_empty => false, :merge => true

  Log.low "BioMart query: '#{main}' [#{(attrs || []) * ', '}] [#{(filters || []) * ', '}] #{open_options.inspect}"

  max_items = 2
  chunks = []
  chunk = []
  attrs.each{|a|
    chunk << a
    if chunk.length == max_items
      chunks << chunk
      chunk = []
    end
  }

  chunks << chunk if chunk.any?

  chunks << [] if chunks.empty?

  Log.low "Chunks: #{chunks.length}"
  if chunks.any?
    chunks.each_with_index{|chunk,i|
      Log.low "Chunk #{ i + 1 } / #{chunks.length}: [#{chunk * ", "}]"
      data = get(database, main, chunk, filters, data, open_options.dup)
    }
  else
    data = get(database, main, [], filters, data, open_options.dup)
  end

  open_options[:filename] = "BioMart[#{main}+#{attrs.length}]"
  if filename.nil?
    results = TSV.open data, open_options
    results.key_field = main
    results.fields = attrs
    results
  else
    Open.write(filename) do |f|
      f.puts "#: " << Misc.hash2string(TSV::ENTRIES.collect{|key| [key, open_options[key]]})
      if field_names.nil?
        f.puts "#" << [main, attrs].flatten * "\t"
      else
        f.puts "#" << field_names * "\t"
      end
      f.write Open.read(data)
    end
    FileUtils.rm data
    filename
  end
end