If you had used the strictures:

use warnings;
use strict;
[download]

you would have gotten these error messages:

Bareword "DUMMYHUGO" not allowed while "strict subs" in use ...
Bareword "DUMMY_GENEFILE" not allowed while "strict subs" in use...
[download]

This would have lead you to suspect some kind of problem with these lines of code:

@hugo = DUMMYHUGO;
    @genes = DUMMY_GENEFILE;
[download]

It is not really clear what you are trying to do, but if you are trying to match names in the genes file to any name on any line of the hugo file, the following code might be a step in the right direction. Please note that this is not an attempt at a complete solution:

#!/usr/bin/env perl
use warnings;
use strict;

my @hugos;
open my $DUMMYHUGO, '<', 'DummyHugo.txt' or die "cannot open file cont
+aining HUGO IDs: $!\n";
while (<$DUMMYHUGO>) {
    my @hugo = split;
    push @hugos, [@hugo];
}
close $DUMMYHUGO;

my $outfile = 'HUGO_dummyResults.txt';
open my $OUT,            '>', $outfile          or die "cannot create 
+the output file: $!\n";
open my $DUMMY_GENEFILE, '<', 'DummyGenes.txt'  or die "cannot open fi
+le containing genes: $!\n";
while (<$DUMMY_GENEFILE>) {
    my @genes = split;
    for my $href (@hugos) {
        my @hugo = @{$href};
        for (my $i = 5; $i < 9; $i++) {
            if ($genes[2] eq $hugo[$i]) {
                print $OUT "$genes[0]\t$genes[1]\t$genes[2]\t$genes[3]
+\t$hugo[1]\n";
            }
        }
    }
}
close $DUMMY_GENEFILE;
close $OUT;
exit;
[download]

The output file will then contain:

ID1    Id2    Katie    Path    KJRJ
ID1a    Id2a    Dave    Path    DJL
ID1b    Id2b    Kean    Path    PKKJ
ID1c    Id2c    Paul    Path    PKKJ
ID1d    Id2d    Sandra    Path    SKJ
[download]

This code reads the hugo file into an array of arrays, @hugos, then reads the genes file one line at a time and checks if the gene name matches any name on any line in the hugo file.

I hope this helps.

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