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

# Fake up a couple of files
my $file_a = <<TXT;
a1\tb1\tc1\td1
a2\tb2\tc2\td2
a3\tb3\tc3\td3
TXT
my $file_b = <<TXT;
starting form the top of the file I need 1. to get the the value in the 3rd
column (c1)

2. search in a second file (file_B.txt, not tab delimited and quite messy) all
the matches for it.

3. when a match is found, I would like to append to the current value (c1), the
value of 4th column (d1) in file_A.txt, separated by a space.

4. go back to the first file (file_A.txt), get the the value in the 3rd column
in the second row (c2) and do another round of search and insert the value of d2
in the second file (file_B.txt).
TXT

# Now the 'real' work - \$file_b treats $file_b as a file
open my $inB, '<', \$file_b or die "Can't open file_b: $!";
my $fileBStr = do {local $/; <$inB>}; # Slurp in all of file_b
close $inB;

open my $inA, '<', \$file_a or die "Can't open file_a: $!";

while (<$inA>) {
    chomp;
    
    my @parts = split /\t/;
    
    next if @parts < 4;
    
    $fileBStr =~ s/\b $parts[2] \b/$parts[2] $parts[3]/xgm;
}

close $inA;

print $fileBStr;

##</code><code>##

starting form the top of the file I need 1. to get the the value in the 3rd
column (c1 d1)

2. search in a second file (file_B.txt, not tab delimited and quite messy) all
the matches for it.

3. when a match is found, I would like to append to the current value (c1 d1), the
value of 4th column (d1) in file_A.txt, separated by a space.

4. go back to the first file (file_A.txt), get the the value in the 3rd column
in the second row (c2 d2) and do another round of search and insert the value of d2
in the second file (file_B.txt).