source: branches/lib/GDE/MAFFT/mafft-7.055-with-extensions/core/makemergetable.rb

#!/bin/env ruby
require 'getopts'

seedoffset = 0

if getopts( "s:" ) == nil ||  ARGV.length == 0 || $OPT_h then
        puts "Usage: #{$0} [-s number_of_seeds] input_files"
        exit
end

if $OPT_s
    seedoffset = $OPT_s.to_i
end


files = ARGV


num = seedoffset + 1
for file in files
        output = ""
        STDERR.puts file
        fp = File.open( file, "r" )
        while line = fp.gets
                if line =~ /^>/ then
                        output += " " + num.to_s
                        num += 1
                end
        end
        fp.close
        puts output + "  # " + file
end