open FILE1,"1.txt" or die "can't open file 1";
open FILE2,"2.txt" or die "can't open file 2";
open(w1,">3.txt");
open(w2,">4.txt");
while (my $line1 = <FILE1>) {
chomp $line1;
my @cond1 = split("\t" , $line1);
print "$cond1[2]\n";
while (my $line2 = <FILE2>) {
chomp $line2;
my @cond2 = split("\t" , $line2);
print "$cond2[2]\n";
if(abs($cond1[2]-$cond2[2])>=2)
{
print w1 "$line1\n";
print w2 "$line2\n";
}
}
}
close FILE1;
close FILE2;
close w1;
close w2;


##</code><code>##

file 1 (1.txt) 
aqw dfr 34 
poilo ggg 98 
file 2  (2.txt)
qww asd 28 
poilo ggg 97  

##</code><code>##

3.txt 
aqw dfr 34
4.txt 
qww asd 28