Class: KnowledgeBase

Inherits:
Object
  • Object
show all
Defined in:
lib/rbbt/matrix/knowledge_base.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#matrix_registry ⇒ Object

Returns the value of attribute matrix_registry.



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# File 'lib/rbbt/matrix/knowledge_base.rb', line 6

def matrix_registry
  @matrix_registry
end

Instance Method Details

#matrix(name) ⇒ Object 



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# File 'lib/rbbt/matrix/knowledge_base.rb', line 11

def matrix(name)
  matrix, options = @matrix_registry[name]

  return matrix if RbbtMatrix === matrix

  Path.setup(matrix) if not Path === matrix and File.exist? matrix

  raise "Registered matrix is strange: #{Misc.fingerprint matrix}" unless Path === matrix

  path = matrix

  raise "Registered path not found: #{path.find}" unless path.exists?
  
  if path.find.directory?
    data, labels, value_type, format, organism, identifiers = Misc.process_options options, :data, :labels, :value_type, :format, :organism, :identifiers 

    data ||= path.data if path.data.exists?
    data ||= path.values if path.values.exists?

    labels ||= path.labels if path.labels.exists?
    labels ||= path.samples if path.samples.exists?

    identifiers ||= path.identifiers if path.identifiers.exists?

    value_type = TSV.parse_header(data.find).key_field if data
    value_type ||= "Unknown ID"

    RbbtMatrix.new data, labels, value_type, format, organism, identifiers
  else
  end
end

#register_matrix(name, matrix, options = {}) ⇒ Object 



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# File 'lib/rbbt/matrix/knowledge_base.rb', line 43

def register_matrix(name, matrix, options = {})
  options = Misc.add_defaults options, :sample_format => "Sample"
  sample_format = Misc.process_options options, :sample_format

  @matrix_registry ||= IndiferentHash.setup({})
  @matrix_registry[name] = [matrix, options]


  register name do
    matrix = matrix(name)
    TSV.read_matrix matrix.data_file, sample_format
  end

  register name.to_s + '_activity' do
    matrix = matrix(name)
    TmpFile.with_file do |tmpfile|
      matrix.activity_cluster(tmpfile)
      tsv = TSV.open(TSV.read_matrix(tmpfile, sample_format))
      tsv.identifiers ||= matrix.data_file.identifier_files.first
      tsv.identifiers = tsv.identifiers.find if tsv.identifiers.respond_to? :find
      
      tsv = tsv.add_field "Activity" do |k,p|
        samples, values = p
        values = values.collect{|v| v.to_i }
        new_values = case Misc.max(values) 
                     when 1
                       [''] * samples.length
                     when 2
                       values.collect{|v| v == 2 ? "active" : '' }
                     else
                       values.collect{|v|
                         case v
                         when 1
                           "inactive"
                         when 2
                           ''
                         else
                           "active"
                         end
                       }
        end
      end

      tsv
    end
  end
end