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open my $file1,"<","1.txt" or die "1.txt: $!\n";
open my $file2,"<","2.txt" or die "2.txt: $!\n";
open my $w1,">","3.txt" or die "3.txt: $!\n";
open my $w2,">","4.txt" or die "4.txt: $!\n";

while (
  defined(my $line1=<$file1>) and defined(my $line2=<$file2>)
...
  print $w2 "$line2\n";
 }
}