ID File1
A 1
C 3
D 4
M 6

ID File2
A 5
B 10
C 15
Z 26

ID File3
A 2
B 6
O 20
X 9

ID  File File2 File3
A 1 5 2 
B 0 10 6
C 3 15 0
D 4 0 0
M 6 0 0 
O 0 0 20
X 0 0 9
Z 0 26 0

#!/usr/bin/perl -w

use strict;

my $Fname1="./path/file1.txt"; #tab delimited format 
my $Fname2="./path/file2.txt";
my $Fname3="./path/file3.txt";

my %combinedfile;
my key;

open(F1, "<$Fname1") or die "Cann't find the input file $Fname1 becuase of $!";
while (my line1 = <F1>) {
  chomp ($line1);
my ($ID1, $count)=split("\t", $line1);
$key=$ID1;
$combinedfile{$key}=$count;
}
close (F1);

open(F2, "<$Fname2") or die "Cann't find the input file $Fname1 becuase of $!";
while (my line2 = <F2>) {
  chomp ($line2);
my ($ID2, $count2)=split("\t", $line2);
$key=$ID2;
if (exists($combinedfile{$key}
 { $combinedfile{$key}.="\n$count2";}
else {
 $combinedfile{$key}="0\n$count2";
}
close (F2);

open(F3, "<$Fname3") or die "Cann't find the input file $Fname1 becuase of $!";
 while (my line3 = <F3>) {
   chomp ($line3);
 my ($ID3, $count3)=split("\t", $line3);
 $key=$ID3;
if (exists($combinedfile{$key}
 { $combinedfile{$key}.="\n$count3";}
else {
 $combinedfile{$key}="0\n0\n$count3";
}
close (F3);

foreach (my $member (keys %combinedfile)){
 split ("/n", $combinedfile{$member));
print $member, "\t", (join("\t", split ("/n", $combinedfile{$member)), "\n";
}

 ID File File2 File3
A 1 5 2 
B 0 10 6
C 3 15 
D 4
M 6
O 0 0 20
X 0 0 9
Z 0 26

D 4\n0

D 4\n0\n0