Perl 5 times

gistfile1.txt

$ perl6 -e 'srand(2); my $f = "genome.fa".IO.open(:w); while $f.tell < 150_000_000 { $f.put(">" ~ flat("A".."Z", "a".."z", "0".."9", "_", "-").roll((5..7).pick).join); $f.put(<A C G T>.roll(80).join()) for ^(3..16).pick }'

$ time perl genome.pl < genome.fa

real	0m2.019s
user	0m1.709s
sys	0m0.280s

$ cat genome.pl
use strict;
use warnings;

my %sequences;
my $current_seqid;
my $current_comment;
my $current_sequence;

sub parse_header {
    my ($header) = @_;
    ($current_seqid, $current_comment) = split / /, $header;
}

# Deal with first sequence
parse_header(scalar <>);

while (my $line = <>) {
    chomp $line;
    if ($line =~ /^>/) {
        $sequences{$current_seqid} = $current_sequence;
        parse_header($line);
        $current_sequence = '';
    } else {
        $current_sequence .= $line;
    }
}