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Save as chunks.pl
Run as perl chunks.pl chunks.data


#!/usr/bin/perl
#
use strict;
use warnings;

my @chunks;
my $lines = 0;
while(<>){
my @parts = split;
push...

Maybe something more like:
awk '
{ for(i = 1; i <= NF; i++) {
f[NR % 4, i] = $i
}
}
!(NR % 4) {
ocnt = 0
for(i = 1; i <= NF; i++)
if(!(f[3, i] in of)) {
of[f[3, i]]...

We don't need or want you to post sensitive data. But, for us to help you write code to process data, we absolutely require a clear description and/or a representative sample (with sensitive data...

That value is 0 as there's text string inside the parentheses. Wouldn't it have been nice if the real data had been known from the beginning?

awk -F"(" ' # make "(" the field separator

FOUND {while (/\\$/) {getline X # if last line had "index_2", read and append
...