phase.rb

#!/usr/bin/env ruby

require 'csv'

FILE1, FILE2, FILE3 = ARGV

HEADER = [ 'RSID', 'CHROMOSOME' , 'POSITION' , 'RESULT' ]

def phase(file1, file2)
    csv1 = CSV.read(file1)[1..-1]
    csv2 = CSV.read(file2)[1..-1]

    csv1.each_with_index.map do |l, i|
        l[3] = (l[3].split('') & csv2[i][3].split('')).join.ljust(2, '-')
        l
    end
end


CSV.open(FILE3, 'w') do |csv|
    csv << HEADER
    phase(FILE1, FILE2).each do |l|
        csv << l
    end
end