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c:\>perl t.pl
-p
...
value of $contig
-o
value of $alignment

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

...
   '-o', $outfile            
);
0 == system @command or die "system @command failed: $?";

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

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

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

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