#!/usr/bin/env perl -l

use strict;
use warnings;

use Inline::Files;

my %found;
/^>(.*)\Z/ and $found{$1} = 0 while <REFERENCE_FILE>;
my $re = '\b(' . join('|' => keys %found) . ')\b';

while (<SEARCH_FILE>) {
    ++$found{$1} while /$re/g;
}

print "$_ occurs: $found{$_}" for sort keys %found;

__REFERENCE_FILE__
>Apple
ignored blah blah blah
>Banana
ignored blah blah blah
>Grape
ignored blah blah blah
__SEARCH_FILE__
Apple Banana Avocado Orange
Grape Apple
Apple Banana Banana