#!/usr/bin/perl -w
use strict

##</code><code>##

#!/usr/bin/perl -w
use strict;

my $prog   = "C:\\path\to\\RNAfold";
my $infile = "C:\\path\\to\\infile";
my $outfile= "C:\\path\\to\\outfile";
my @args   = qw/ -p noOUTPUTFILE /;

print "Executing with one arg system\n";
my $return_value = system("$prog $infile $outfile");
if ($return_value == 0) {
    print "Success!\n";
}
else {
    printf "Failed with error code %d\nError message: $?\n", 
        $return_value>>8;
}

print "Executing with muti arg system\n";
$return_value = system($prog, $infile, $outfile);
# or
$return_value = system($prog, @args);
# check how it went by checking return_value as above

print "Executing $prog $infile $outfile with backtics\n";
my $screenoutput = `$prog $infile $outfile`;
print "Got $screenoutput\n";
# check how it went by checking $?
die "Got error $?\n" if $?