use Modern::Perl;
use autodie;

sub count_seq {
    my ($file, $search_seq) = @_;
    my $sequence;
    {
        local $/; # slurp mode
        open my $fh, '<', $file;
        $sequence = <$fh>;
    }
    $sequence =~ s/[\s\n]//g;
    return scalar (()=$sequence=~ m/$search_seq/g);
}

say count_seq('test.file', 'TA');