#!/usr/bin/env perl -l

use strict;
use warnings;

/^[^>]/ && do { y/N/ /; print join "\n" => split } while <DATA>;

__DATA__
>fasta1
NNNAGTCTGCAAANAATTTGCGGCTCACAAT
>fasta2
CGCAGCCATTAACATCTCAACAAGCCAAAAATTCCTTCTCAGAAATTCGGNNN
>mytest1
NNNACGTNNTGCANN
>mytest2
ACGTNNCGTANNNNNGTACNTACG
>mytest3
TGCA

##</code><code>##

AGTCTGCAAA
AATTTGCGGCTCACAAT
CGCAGCCATTAACATCTCAACAAGCCAAAAATTCCTTCTCAGAAATTCGG
ACGT
TGCA
ACGT
CGTA
GTAC
TACG
TGCA