Include matrix conversion for R

[seanmcallister]

Please consider packaging the "seanie_matrix_convert.rb" with this repository so people can convert the output to a pairwise matrix for visualization in R.

[mooreryan]

@seanmcallister Do you have a copy of that script?

[seanmcallister]

Here you go. If you include, I would change 2 things for use in R:

1. Output the self comparisons as 100 instead of 0.
2. For this aai, there are two matrices that would be useful. One for the one way hits (A->B on upper triangle, B->A on lower triangle), and one for the two way hits (output both upper and lower triangles of the matrix instead of leaving the lower triangle as 0's; the upper triangle in this case would be identical to the lower triangle).

# take 3 col dist matrix and spit out a dist matrix for R

dists = {}
all = []
File.open(ARGV.first).each_line.with_index do |line, lineno|
  unless lineno.zero?
    row, col, dist = line.chomp.split "\t"
    dist = dist.to_f

    all << row << col

    unless dists.has_key? row
      dists[row] = Hash.new 0
    end

    dists[row][col] = dist
  end
end

all = all.uniq.sort

puts ["", all].flatten.join "\t"

all.each_with_index do |row, ridx|
  row_name = all[ridx]
  print row_name

  all.each do |col|
    dist = 0
    dist = dists[row][col] if dists.has_key?(row)

    printf "\t%s", dist
  end

  puts
end