mergefile.1

##</code><code>##

15    20    foo
22    30    bar
30    33    baz
14    22    fubar

##</code><code>##

mergefile.2

##</code><code>##

alpha    baz    17.30
gamma    foobar    22.35
gamma    bar    19.01
delta    fromish    33.03
sigma    bear    14.56

##</code><code>##

mergefile.out
bar     22      30      gamma   19.01
baz     30      33      alpha   17.30
bear    null    null    sigma   14.56
foo     15      20      null    null
foobar  null    null    gamma   22.35
fromish null    null    delta   33.03
fubar   14      22      null    null

##</code><code>##

#!/usr/bin/perl -w
use strict;
use warnings;

##</code><code>##

open F1, 'sort -k3 mergefile.1|' or die "opening file 1";
open F2, 'sort -k2 mergefile.2|' or die "opening file 2";

##</code><code>##

open OUF, '>', 'mergefile.out' or die "opening output file";

##</code><code>##

my @in1;
my @in2;

##</code><code>##

sub getrec1 {
        @in1 = ();
        if (!eof(F1)) {
                (@in1) = split /\t/, <F1>;
                chomp $in1[2];
        }
}

##</code><code>##

sub getrec2 {
        @in2 = ();
        if (!eof(F2)) {
                (@in2) = split /\t/, <F2>;
                chomp $in2[2];
        }
}

##</code><code>##

sub write1 {
        print OUF "$in1[2]\t$in1[0]\t$in1[1]\tnull\tnull\n";
        getrec1;
}

##</code><code>##

sub write2 {
        print OUF "$in2[1]\tnull\tnull\t$in2[0]\t$in2[2]\n";
        getrec2;
}

##</code><code>##

sub writeboth {
        print OUF "$in1[2]\t$in1[0]\t$in1[1]\t$in2[0]\t$in2[2]\n";
        getrec1;
        getrec2;
}

##</code><code>##

# Prime the pump
getrec1;
getrec2;

##</code><code>##

while (1) {
        last if $#in1<0 and $#in2<0;

##</code><code>##

        if ($#in1<0 or $#in2<0) {
                # Only one file is left...
                write2 if $#in1<0;
                write1 if $#in2<0;
        }
        elsif ($in1[2] eq $in2[1]) {
                # Matching records, merge & write 'em
                writeboth;
        }
        elsif ($in1[2] lt $in2[1]) {
                # unmatched item in file 1, write it & get next rec
                write1;
        }
        else {
                # unmatched item in file 2, write it & get next rec
                write2;
        }
}

##</code><code>##

bar    null    null    gamma    19.01
bar    22    30    null    null
baz    null    null    alpha    17.30
baz    30    33    null    null
bear    null    null    sigma    14.56
foo    15    20    null    null
foobar    null    null    gamma    22.35
fromish    null    null    delta    33.03
fubar    14    22    null    null

##</code><code>##

I altered the line "chomp $in2[2];" to read "chomp $in2[1];"