One approach is to read the 3rd and 4th columns of file A into a hash, then for each line of file B, loop through the hash keys, making the substitutions. 
use strict;
use warnings;

my $fhi;

my %data;
open $fhi, '<', 'file_A.txt' or die "can not open file file_A.txt: $!"
+;
while (<$fhi>) {
    chomp;
    my @cols = split /\t/;
    $data{$cols[2]} = "@cols[2..3]";
}
close $fhi;

open    $fhi, '<', 'file_B.txt'     or die "can not open file file_B.t
+xt: $!";
open my $fho, '>', 'file_B_out.txt' or die "can not open file file_B_o
+ut.txt: $!";
while (<$fhi>) {
    for my $k (keys %data) {
        s/$k/$data{$k}/g;
    }
    print $fho $_;
}
close $fho;

[download]
One functional flaw with your solution is that you keep overwriting your output file every time you open it for output. Thus, you lose the results of your previous substitution.

Update: I like almut's $search string better than my for loop.

In reply to Re: Get data from a file to search and replace within a second file by toolic
in thread Get data from a file to search and replace within a second file by biscardi

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