Something like this? 

#!/usr/bin/perl

# https://perlmonks.org/?node_id=1228191

use strict;
use warnings;

my $window = 1e6;
my $A = my $C = my $G = my $T = my $all = 0;
my (@sizes, $tmp, $start);

sub letter
  {
  my $n = rand $all--;
  $n < $A ? ($A--, return 'a') :
    $n < $A + $C ? ($C--, return 'c') :
    $n < $A + $C + $G ? ($G--, return 'g') :
    ($T--, return 't');
  }

sub output
  {
  for my $count ( @sizes )
    {
    print ">ID", $start++, "\n";
    print map(letter(), 1 .. $count), "\n";
    }
  @sizes = ();
  }

while( <DATA> )
  {
  $start //= s/\D+//gr;
  $_ = <DATA>;
  $A += tr/a//;
  $C += tr/c//;
  $G += tr/g//;
  $T += tr/t//;
  $all += $tmp = tr/acgt//;
  push @sizes, $tmp;
  $all >= $window and output();
  }
$all and output();

__DATA__
>ID1
atgagcagctag
>ID2
tggacgagctgaca
>ID3
tgactagacggacatac

[download]

In reply to Re: Reduce RAM required by tybalt89
in thread Reduce RAM required by onlyIDleft

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