It's your fault :)

In your original post, you showed the input as LOWER CASE. Your actual data file has input in UPPER CASE.

Here's a version that handles upper case. 

#!/usr/bin/perl

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

use strict;
use warnings;

my $window = 1e6;
my $A = my $C = my $G = my $all = 0;
my (@sizes, $tmp, $start);
my $inputfile = shift //  'd.1228191';
my $outputfile = shift // 'd.out.1228191';

open my $in, '<', $inputfile or die "$! opening $inputfile";
open my $out, '>', $outputfile or die "$! opening $outputfile";

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

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

while( <$in> )
  {
  if( /^>/ )
    {
    $start //= s/\D+//gr;
    }
  elsif( /^[ACGT]/ )
    {
    $A += tr/A//;
    $C += tr/C//;
    $G += tr/G//;
    $all += $tmp = tr/ACGT//;
    push @sizes, $tmp;
    $all >= $window and output();
    }
  }
$all and output();
close $in;
close $out;

[download]

In reply to Re^9: Reduce RAM required by tybalt89
in thread Reduce RAM required by onlyIDleft

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