#!/usr/bin/perl

 use strict;
 use warnings;

my $outfile = "HUGO_dummyResults.txt";

open( OUT, "> $outfile" ) or die "cannot create the output file";

open (DUMMY_GENEFILE, 'DummyGenes.txt') or die "cannot open file containing genes";

open (DUMMYHUGO,'DummyHugo.txt') or die "cannot open file containing HUGO IDs";

#################################################
#Operations
#################################################

#make array HUGO
my @hugo = <DUMMYHUGO>;

foreach (<DUMMY_GENEFILE>) #Changed from (<DUMMY_GENEFILE>)

{
    #make array genes
    my @genes = split ( /\b/, $_ );
    
    foreach my $i ( 4 .. 7 )   
    {
      if ($genes[2] eq $hugo[$i])
      {
        print OUT "$genes[0]\t$genes[1]\t$genes[2]\t$genes[3]\t$hugo[1]\n";
      }
            
      print OUT "$genes[0]\t$genes[1]\t$genes[2]\t$genes[3]\tNo HUGO ID\n";
    }    
    
    
}
close (DUMMYHUGO);
close (DUMMY_GENEFILE);
close (OUT);
exit;    


##</code><code>##

ID1             Id2             No HUGO ID
ID1             Id2             No HUGO ID
ID1             Id2             No HUGO ID
ID1             Id2             No HUGO ID
ID1a            Id2a            No HUGO ID
ID1a            Id2a            No HUGO ID
ID1a            Id2a            No HUGO ID
ID1a            Id2a            No HUGO ID
ID1b            Id2b            No HUGO ID
ID1b            Id2b            No HUGO ID
ID1b            Id2b            No HUGO ID
ID1b            Id2b            No HUGO ID
ID1c            Id2c            No HUGO ID
ID1c            Id2c            No HUGO ID
ID1c            Id2c            No HUGO ID
ID1c            Id2c            No HUGO ID
ID1d            Id2d            No HUGO ID
ID1d            Id2d            No HUGO ID
ID1d            Id2d            No HUGO ID
ID1d            Id2d            No HUGO ID