print 'ACGT' | ' ';;
acgt
####
$s = 'GGTACACAGAAGCCAAAGCAGGCTCCAGGCTCTGAGCTGTCAGCACAGAGACCGAT';;
$m = 'GGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT';;
( $mm = $m ) =~ tr[N][\x20];;
print $mm;;
GGT T
print $s | $mm;;
GGTacacagaagccaaagcaggctccaggctctgagctgtcagcacagagaccgaT
##
##
#! perl -slw
use strict;
open SEQ, '<', 'data1.dat' or die $!;
open MASK, '<', 'data2.dat' or die $!;
while( my $seq = ) { ## Read a sequence
my $mask = ; ## And the corresponding mask
$mask =~ tr[N][ ]; ## Ns => spaces
print $seq | $mask; ## bitwise-OR them and print the result
}
close SEQ;
close MASK;