First, split takes a regular expression, not a string (except sometimes ;-). So splitting on '\t' won't give the expected results. Next, I suspect that @id_list grows fairly long over time, and you are iterating over the entire array with grep. A hash is more suitable here: 

use strict;
use warnings;


my $name = '';
my %id_list;

open (STDIN,"perl first_program.pl|") || die "$!";
open (OUT, ">", "out.txt") || die "$!";

while(my $line_in =<STDIN>){
  chomp($line_in);
  my @line_array = split(/\t/,$line_in);
  my @subline_array = split(/\|/, $line_array[1]);

  unless ($name eq $line_array[0]) {
    %id_list = ();
    $name = $line_array[0];  
  }
  next if $id_list{$subline_array[3]}++;
  print OUT "$line_in\n";
}

[download]

If you experience memory shortage, tie the hash %id_list to a disk file via e.g. DB_File.

In reply to Re: slow parser how to make it faster by shmem
in thread slow parser how to make it faster by baxy77bax

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