c:\>perl t.pl
-p
blastn
-d
value of $hu_seq value of $hd_seq
-i
value of $contig
-o
value of $alignment

##</code><code>##

my $outfile = '\"c:\Documents and Settings\foo\my file\"';

my @command = (
   $^X, '-leprint for @ARGV', '--',
   '-o', $outfile            
);
0 == system @command or die "system @command failed: $?";

##</code><code>##

c:\>perl t.pl
-o
"c:\Documents
and
Settings\foo\my
file"

##</code><code>##

my $outfile = '\"c:\Documents and Settings\foo\my file\"';

my $command = qq($^X -le"print for \@ARGV" -- -o "$outfile");
0 == system $command or die "system $command failed: $?";

__END__
-o
"c:\Documents and Settings\foo\my file"

##</code><code>##

my $outfile = '"\"c:\Documents and Settings\foo\my file\""';