#!/usr/bin/perl -w

use strict;
use warnings;
use vars qw(%origins);

if( @ARGV < 3){
      print "usage: A message here\n";
      exit 0;
}

open(INPUT1,$ARGV[0]) || die "Cannot open file \"$ARGV[0]\""; #Orginal IDs and four letter codes
open(INPUT2,$ARGV[1]) || die "Cannot open file \"$ARGV[1]\""; #Orginal IDs in the second column
open(RESULTS,">$ARGV[2]")|| die "Cannot open the Results file \"$ARGV[2]\""; # Origanl IDs will change to four letter code

my %origins;

while (<INPUT1>) {
    chomp;
    my @columns = split '\t';
    $origins{$columns[0]} = $columns[1];

}

close(INPUT1);

while (<INPUT2>) {
    chomp;
    (my $bioC, my $contig_id , my $pip) = split("\t", $_);
     for my $oKey (sort keys %origins) {
        my $origin = $origins{$oKey};
     if ($contig_id eq $oKey){
     print RESULTS "$bioC\t$origin\t$pip\n";
     #print "$bioC\t$origin\t$pip\n";
     }
   }
}
close(INPUT2);
close(RESULTS);