use strict;
    use warnings;
use File::Find;
use Net::FTP;
use Cwd;

my $ftp = Net::FTP->new("ftp.ncbi.nih.gov", Timeout => 30) or die "Cannot connect to server: $@";   

my $dir = "/genomes/Bacteria";
$ftp->cwd($dir) or die "Cannot cd to " , $dir;
my @directories = $ftp->ls() or die "cannot list any DIRs";
my @files;
find( sub { push @files, $File::Find::name if /\.fna$/ }, @directories ) or die "can't find shit";    	

for(my $i=0; $i<@files; $i++){
print "$i","x hooray"
}

$ftp->quit;

##</code><code>##

use warnings;                                  
use strict;
use Net::FTP;

my $ftp = Net::FTP->new("ftp.ncbi.nih.gov", Timeout => 30) or die "Cannot connect to server: $@";   

## login is mandatory, even if no user and password is specified:
$ftp->login("anonymous",'-anonymous@') or die "Cannot login ", $ftp->message;

my $dir = '/genomes/Bacteria';

## move to the subdirectory:
$ftp->cwd($dir) or die "Cannot cd to " , $ftp->message();
#print "part 1\n";

my @dir_listing = $ftp->ls() or die $ftp->message;
## note: you need to save DIRs as arrays before you can search for specific 
## files or anything

my @files;
for(my $j=0; $j<@dir_listing; $j++){
	##list all the files in subdirs:
	my @file_list = $ftp-> ls($dir_listing[$j]) or die $ftp->message;
	##weed out all the files you want and put them in an array
	my @found_files = grep(/.fna/, @file_list);
	push (@files, @found_files);
	}

##Make a resultfile to print all the files to:
my $results = "D:/Genomes/results/filelist.dat";   									
open (OUTFILE, '>', $results)  or die "Cannot write $!n"; 	
	
for(my $i=0; $i<@files; $i++){
print OUTFILE "@files[$i]";
}
      
close (OUTFILE);

$ftp->quit;