I have some general advice for you, but I'll wait till I'm sober. Till then:

use strict;
use warnings;

my %data;

open (DATA1, "<", "data1.txt") or die "cannot open file";

while (<DATA1>) {
    my @line = split (/\t/, $_);
    $data{$line[0]} = $line[1];
}

my @k = keys %data;
foreach my $key (@k) {
    print "$key, $data{$key}\n";
}
close DATA1;

open (DATA2, "<", "data2.txt") or die "cannot open file";
print "found:\n";

while (<DATA2>) {
chomp;
if (exists $data{"$_"}) {print "$data{$_}\n";}

close DATA2;
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This doesn't check duplicates, is too verbose, but I hope it'll help.