#!/usr/local/bin/perl

# multifileout.pl

use strict;
use warnings;

my @file_ends = qw{./ .fasta};
my %handle = ();
my @ko_array = qw(abc def ghi);

while (<DATA>) {
    chomp;
    my ($head, $seq) = split / /;

    for my $ko (@ko_array) {
        if ($head =~ m/$ko/) {
            if (! exists $handle{$head}) {
                open my $fh, q{>>}, join($ko, @file_ends);
                $handle{$head} = $fh;
            }
            print { $handle{$head} } qq{$head\n$seq\n};
        }
    }
}

map { close $handle{$_} } keys %handle;

__DATA__
abc a123
def d123
abc a456
ghi g123
ghi g456
def d456

##</code><code>##

ken@ganymede: ~/tmp
$ ls -l *.fasta
ls: *.fasta: No such file or directory
ken@ganymede: ~/tmp
$ multifileout.pl
ken@ganymede: ~/tmp
$ ls -l *.fasta
-rw-r--r--  1 ken  staff  18  7 Feb 08:29 abc.fasta
-rw-r--r--  1 ken  staff  18  7 Feb 08:29 def.fasta
-rw-r--r--  1 ken  staff  18  7 Feb 08:29 ghi.fasta
ken@ganymede: ~/tmp
$ cat abc.fasta
abc
a123
abc
a456
ken@ganymede: ~/tmp
$ cat def.fasta
def
d123
def
d456
ken@ganymede: ~/tmp
$ cat ghi.fasta
ghi
g123
ghi
g456
ken@ganymede: ~/tmp
$