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

[download]

That would be better as: 

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

[download]


my @file_ends = qw{./ .fasta};
...
                open my $fh, q{>>}, join($ko, @file_ends);

[download]

With three argument open you don't need to prepend the file name with "./" and you should always verify that the file successfully opened before trying to use a possibly invalid filehandle: 

my file_end = '.fasta';
...
                open my $fh, '>>', "$ko$file_end" or die "Cannot open 
+'$ko$file_end' because: $!";

[download]

In reply to Re^2: Write to multiple files by jwkrahn
in thread Write to multiple files by julio_514

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