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#cat variable.txt
NEGATIVE=3
NEG-DID=2
NEG-WARN=4
# cat file.txt
2860377|"DATA1"|"DATA2"|"65343"|"DATA2"|"DATA4"|"11"|"DATA5"|"DATA6"|"65343"|"DATA7"|"0"|"8"|"1"|"NEGATIVE"...

awk -F\| '{sub("\"NEGATIVE\"",3,$15);sub("\"NEG-DID\"",2,$15);sub("\"NEG-WARN\"",4,$15)}1' OFS="|" test.txt

Here is one way of doing it

$ cat infile.txt
123 abc defDOERAEMEaea
fsfsfsf sdsdfsa

$ cat example.pl
#!/usr/local/bin/perl

use strict;
use warnings;

my $file = "infile.txt";
my...