use strict;
use warnings;
use Bio::FASTASequence::File;
use File::Find::Rule;

my @ffns = File::Find::Rule->file->name( '*.ffn' )->in( '.' );

my %result;
my $output = 'org.fasta';

my $bff = Bio::FASTASequence::File->new;
for my $ffn ( @ffns ) {
    my $parsed = $bff->file( $ffn );

    for my $orga ( keys %{$parsed} ) {
        my $subsequence = substr $parsed->{$orga}->getSequence(), 3, 24;
        my ($name)      = $parsed->{$orga}->getDescription() =~ m{ \[ (.*?) \] }x;

        push @{ $result{$name} }, $subsequence;
    }
}

open my $fh, '>', $output;
for my $key ( sort keys %result ) {
    print $fh "> $key\n", join( '', @{ $result{$key} } ),"\n";
}
close $fh;