Or without a loop (also untested):

use strict; # Always
use IO::File; # I like to localize filehandles.

sub CountPatternInFile
{
    local $/;
    my ( $filename, $pattern, $stop_pattern ) = @_;
    my $fh = IO::File->new( $filename ) or die $!;
    $_ = <$fh>;
    close $fh or warn $!;
    ($_) = split /$stop_pattern/;
    return s/($pattern)/$1/g;
}
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