#!/usr/bin/perl

use warnings;
use strict;

my $infile=$ARGV[0];
my $header;
my %sequence=();

open FASTA, $infile or die "Couldn't open fasta-file";
open (OUTFILE,">fasta_report.txt");

# Populate a hash with the fasta-data
# fasta example:
#>fasta1
#NNNAGTCTGCAAANAATTTGCGGCTCACAAT
#>fasta2
#CGCAGCCATTAACATCTCAACAAGCCAAAAATTCCTTCTCAGAAATTCGGNNN

while (<FASTA>) {
  chomp;
  if (/^>(.*)$/){
    $header=$1;
  }
  elsif (/^(\S+)$/){
    $sequence{$header} .= $1 if $header;
  }
}
close FASTA;

#Go through the hash and split at Ns
foreach my $key (keys %sequence){ 
  my @contigs = split (/N+/, $sequence{$key});
  foreach my $element (@contigs){
    print OUTFILE "$element\n";
  }
}  
close OUTFILE;