G'day ic23oluk,

Here's my take on a solution (pm_1191418_file_merge.pl): 

#!/usr/bin/env perl -l

use strict;
use warnings;
use autodie;

die "Usage: $0 file1 file2\n" unless @ARGV == 2;

my (@fhs, $shorter);

for (@ARGV) {
    die "'$_' is zero-length\n" if -z;
    open my $fh, '<', $_;
    push @fhs, $fh;
}

LOOP: while (1) {
    my @out_line;

    for (0 .. 1) {
        my $line = readline $fhs[$_];

        if (! defined $line) {
            $shorter = $_ unless defined $shorter;
            last LOOP if $shorter != $_;
            seek $fhs[$_], 0, 0;
            $line = readline $fhs[$_];
        }

        push @out_line, $line;
    }

    chomp @out_line;
    print @out_line;
}

[download]

I created four input files: one empty; one with just a single newline; the other two with data. 

$ ls -al pm_1191418_data_*
-rw-r--r-- 1 ken staff  1 May 29 16:57 pm_1191418_data_blank.txt
-rw-r--r-- 1 ken staff 24 May 29 16:14 pm_1191418_data_five.txt
-rw-r--r-- 1 ken staff  8 May 29 16:14 pm_1191418_data_two.txt
-rw-r--r-- 1 ken staff  0 May 29 16:47 pm_1191418_data_zero.txt
$ cat pm_1191418_data_zero.txt
$ cat pm_1191418_data_blank.txt

$ cat pm_1191418_data_two.txt
ONE
TWO
$ cat pm_1191418_data_five.txt
one
two
three
four
five

[download]

These first two runs just exercise the sanity tests: 

$ pm_1191418_file_merge.pl
Usage: ./pm_1191418_file_merge.pl file1 file2
$ pm_1191418_file_merge.pl pm_1191418_data_zero.txt pm_1191418_data_tw
+o.txt
'pm_1191418_data_zero.txt' is zero-length

[download]

The remaining runs test blank lines; files with a different number of lines in either order; and files with the same number of lines: 

$ pm_1191418_file_merge.pl pm_1191418_data_blank.txt pm_1191418_data_t
+wo.txt
ONE
TWO
$ pm_1191418_file_merge.pl pm_1191418_data_two.txt pm_1191418_data_bla
+nk.txt
ONE
TWO
$ pm_1191418_file_merge.pl pm_1191418_data_two.txt pm_1191418_data_fiv
+e.txt
ONEone
TWOtwo
ONEthree
TWOfour
ONEfive
$ pm_1191418_file_merge.pl pm_1191418_data_five.txt pm_1191418_data_tw
+o.txt
oneONE
twoTWO
threeONE
fourTWO
fiveONE
$ pm_1191418_file_merge.pl pm_1191418_data_blank.txt pm_1191418_data_b
+lank.txt

$ pm_1191418_file_merge.pl pm_1191418_data_two.txt pm_1191418_data_two
+.txt
ONEONE
TWOTWO

[download]

— Ken

In reply to Re: writing two files (different in length) to one output by kcott
in thread writing two files (different in length) to one output by ic23oluk

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