G'day wackattack,

"I'm using arrays because these are big files (gigabytes) and I need to do thousands of searches without having to load the file from hard drive each time."

I would neither load the file into an array nor read it, in its entirety, from disk (any number of times). Instead, reading a file of this size line by line, would probably be a better option. Here's how I might tackle this task.

#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

my $file_to_search = 'file_to_search';
my $file_of_search_terms = 'file_of_search_terms';
my $file_of_search_counts = 'file_of_search_counts';

my %count;

{
    open my $search_terms_fh, '<', $file_of_search_terms;
    %count = map { chomp; $_ => 0 } <$search_terms_fh>;
}

my @search_terms = keys %count;

{
    open my $in_fh, '<', $file_to_search;

    while (<$in_fh>) {
        chomp;
        next if -1 == index $_, 'Z';

        for my $search_term (@search_terms) {
            next if -1 == index $_, $search_term;
            ++$count{$search_term};
            last;
        }
    }
}

{
    open my $out_fh, '>', $file_of_search_counts;
    print $out_fh "$_ : $count{$_}\n" for sort @search_terms;
}
[download]

I used this dummy data for testing:

$ cat file_to_search
100008020Z
Z100008020
100008020
100008030Z
Z100008030
100008030
100008040Z
Z100008040
100008040
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$ cat file_of_search_terms
100008010
100008020
100008030
100008040
100008050
[download]

Here's the output:

$ cat file_of_search_counts
100008010 : 0
100008020 : 2
100008030 : 2
100008040 : 2
100008050 : 0
[download]