my $infile = 'path/to/file';
my $out1 = 'path/to/out1';
my $out2 = 'path/to/out2';

open(R_FILE,"<$infile") or die$!;
my @lines = <R_FILE>;
close R_FILE;

open(W_OUT1,">$out1") or die $!;
open(W_OUT2,">$out2") or die $!;
for(my $i = 0; $i < $#lines; $i +=2){
  print W_OUT1 $lines[$i];
  print W_OUT2 $lines[$i+2];
}
close W_OUT1;
close W_OUT2;