#!/usr/bin/perl
use strict;
use Data::Dumper;
#use Data::Dump 'pp';

my %data = ();
my ($key1,$key2);
while (<DATA>){
  chomp;
  next unless /\S/; #skip blank lines
  my @col = split ',',$_; #column1 is $col[0]
  if (@col == 2){
    ($key1,$key2) = @col;
  } else {
    push @{ $data{$key2}{$key1}},\@col;
  }
}
#print pp \%data; # use Data::Dump if installed
print Dumper \%data;

__DATA__
1,1
1,A1,B1,C1,D1
2,A1,B1,C1,D1
3,A1,B1,C1,D1

1,2
1,A2,B2,C2,D2
2,A2,B2,C2,D2
3,A2,B2,C2,D2

1,3
1,A3,B3,C3,D3
2,A3,B3,C3,D3
3,A3,B3,C3,D3