#!/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;