@indices{(keys %index_1),(keys %index_2)}++;

#!/usr/bin/perl

use strict;
use warnings;

open (my $index_1 , '<', $ARGV[0]);
my %index_1;
while (<$index_1>){
        chomp;
        if (/^([CAGT]+)\s(\d+)$/){
                $index_1{$1}=$2;
        }
        else {
                print "Invalid input \"$_\" in $ARGV[0], line $.\n";
        }
}
close $index_1;

open (my $index_2 , '<', $ARGV[1]);
my %index_2;
while (<$index_2>){
        chomp;
        if (/^([CAGT]+)\s(\d+)$/){
                $index_2{$1}=$2;
        }
        else {
                print "Invalid input \"$_\" in $ARGV[1], line $.\n";

        }
}
close $index_2;

open (my $index_3 , '<', $ARGV[2]);
my %index_3;
while (<$index_3>){
        chomp;
        if (/^([CAGT]+)\s(\d+)$/){
                $index_3{$1}=$2;
        }
        else {
                print "Invalid input \"$_\" in $ARGV[2], line $.\n";

        }
}
close $index_3;



my %indices;
@indices{(keys %index_1),(keys %index_2),(keys %index_3)}++;
for my $index (sort (keys %indices)){
        print "$index\t ",$index_1{$index}||"0","\t", $index_2{$index}||"0","\n", $index_3{$index}||"0","\n";
}

AAAAAAACGTCAGGGAAGCTTGTCATG	 3	0
0
AAAAAACCGCCGATGCCTCCGGCCATG	 2	0
0
AAAAAAGTTTTAATCATTATCGACATG	 1	0
0
AAAAACTGTATTCAGTGACCAATCATG	 4	0
0
AAAAAGACAGCTGCTCCAGATAACATG	 1	0
0
AAAAATCTGTAAGGCTAATGGTGCATG	 1	0
0
...