#!/usr/bin/perl

use strict;
use Getopt::Long;

my $input_file_1 = "";
my $input_file_2 = "";
my $iteration = "dot";
my $separator = "\t";

################################################################################
########################## Get the current version of the database and use that

GetOptions( "file_1=s" => \$input_file_1,
            "file_2=s" => \$input_file_2,
            "iteration=s" => \$iteration,
            "separator=s" => \$separator
          );

my $file_identifier_1 =  "<".$input_file_1;
my $file_identifier_2 =  "<".$input_file_2;

open( DATA, "$file_identifier_1" ) || die "$!";
my @array_1 = <DATA>;
close(DATA);

open( DATA, "$file_identifier_2" ) || die "$!";
my @array_2 = <DATA>;
close(DATA);

if($separator eq "")
{
  $separator = "\t";
}
elsif($separator eq "tab")
{
  $separator = "\t";
}
elsif($separator eq "space")
{
  $separator = " ";
}
elsif($separator eq "comma")
{
  $separator = ",";
}
elsif($separator eq "new_line")
{
  $separator = "\n";
}

if($iteration eq "" or $iteration eq "dot")
{
  for(my $i = 0; $i < @array_1; $i++)
  {
    chomp($array_1[$i]);
    print("$array_1[$i]".$separator."$array_2[$i]\n");
  }
}
elsif($iteration eq "cross")
{
  for(my $i = 0; $i < @array_1; $i++)
  {
    for(my $j = 0; $j < @array_2; $j++)
    {
      chomp($array_1[$i]);
      chomp($array_2[$j]);
      print("$array_1[$i]".$separator."$array_2[$j]\n");
    }
  }
}
elsif($iteration ne "cross" or $iteration ne "dot")
{
  print("You may have a spelling mistake in your \niteration option, please input either dot or cross\n");
}