Assuming that there are no two equal lines in one file and files are not too big two simple loops will do the job:
#!/usr/bin/perl
$fnx = "file1";
$fny = "file2";
$fnz = "file.uncommon";
$fntmp = "file.common";
open FPX, "$fnx" or die "Error in write:$!";
open FPY, "$fny" or die "Error in write:$!";
open FPZ, ">$fnz" or die "Error in write:$!";
open FPTMP, ">$fntmp" or die "Error in write:$!";
@x_lines = map {s/^\s+//; s/\s+$//; $_ } <FPX>;
@y_lines = map {s/^\s+//; s/\s+$//; $_ } <FPY>;
for $xnr(1..@x_lines)
{
$x = $x_lines[$xnr-1];
$matched = 0;
for $ynr(1..@y_lines)
{
$y = $y_lines[$ynr-1];
if($x eq $y)
{
print "Saving matched at $xnr\n";
print FPTMP "$x \n";
$matched = 1;
last;
}
}
if(!$matched)
{
print "Saving unmatched at $xnr\n";
print FPZ "$x \n";
}
}
close FPX;
close FPY;
close FPZ;
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