Module: Matr

Defined in:
lib/matr.rb,
lib/matr/version.rb

Constant Summary collapse

VERSION = 
"0.3.0"

Class Method Summary collapse

Class Method Details

.default_opt(opts, key, default) ⇒ Object 



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# File 'lib/matr.rb', line 4

def self.default_opt opts, key, default
  opts.has_key?(key) ? opts[key] : default
end

.main(opts) ⇒ Object 



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# File 'lib/matr.rb', line 8

def self.main opts

  infile               = opts[:infile]
  mode                 = self.default_opt opts, :mode, "ava"
  self_score           = self.default_opt opts, :self_score, 100
  ensure_self_scores   = self.default_opt opts, :ensure_self_scores, true
  no_header = self.default_opt opts, :no_header, false

  if opts[:na_replace_given]
    missing_score = opts[:na_replace]
  else
    missing_score = "na"
  end

  output_style = self.default_opt opts, :output_style, "wide"

  unless File.exist? infile
    raise StandardError, "FATAL -- infile '#{infile}' does not exist"
  end

  unless output_style == "wide" || output_style == "long"
    raise StandardError, "FATAL -- output style must be either wide or long"
  end

  graph    = Hash.new { |ht, k| ht[k] = Hash.new }
  all_keys = Set.new
  header   = nil

  File.open(infile, "rt").each_line.with_index do |line, idx|
    line.chomp!

    if idx.zero? && !no_header
      header = line
    else
      source, target, score = line.split "\t"

      all_keys << source << target

      # If you have duplicates with different scores, that's an error: a
      # => b = 10 and a => b = 20
      if graph[source].has_key?(target) && graph[source][target] != score
        raise StandardError, "FATAL -- source--target (#{source}--#{target}) was repeated with a different score.  Old score was #{graph[source][target]}, and the new score was #{score}."
      end

      graph[source][target] = score

      if mode == "ava_symmetric"
        # Since you might have a files that specifies a => b = 10, and b
        # => a = 10, that would be okay.  But if you have a => b = 10, and
        # b => a = 5, then that would be an error.
        if graph[target].has_key?(source) && graph[target][source] != score
          raise StandardError, "FATAL -- target--source (#{target}--#{source}) is specified seperately from source--target (#{source}--#{target}), BUT their scores do not match.  This means your matrix is NOT symmetric.  Did you really mean to pass the --ensure-symmetry flag?"
        end

        graph[target][source] = score
      end
    end
  end

  all_keys = all_keys.to_a.sort

  # Zip through and add any self scores that weren't added.
  all_keys.each do |source|
    all_keys.each do |target|
      # With ensure_self_scores, we overwrite the self score even if it was already given.  Otherwise, only if it was NOT given.
      if source == target && (ensure_self_scores || !graph[source][target])
        graph[source][target] = self_score
      end
    end
  end

  if output_style == "long"
    puts header unless no_header

    all_keys.each do |source|
      all_keys.each do |target|
        puts [source, target, graph[source][target] || missing_score].join "\t"
      end
    end
  else
    puts ["", all_keys].join "\t"

    all_keys.each do |source|
      row = all_keys.map do |target|
        graph[source][target] || missing_score
      end

      puts [source, row].join "\t"
    end
  end
end