use Data::Dumper;

my @array;
# read from the file handle line by line
while(<DATA>) {
  chomp;

  # split each line by ',' and save
  # corresponding records into the @recs array
  my @recs = split /\,/;

  # loop through the records array..
  for (my $i; $i < @recs; $i++) {

    # and save I-th record in array
    # array[I].  Use @{..} to let push() know
    # that array[I] is also an array.
    push @{$array[$i]}, $recs[$i];
  }
}

print Dumper(\@array);

__DATA__
A,B,C
D,B,C

E,C,C
[download]

$VAR1 = [
          [
            'A',
            'D',
            'E'
          ],
          [
            'B',
            'B',
            'C'
          ],
          [
            'C',
            'C',
            'C'
          ]
        ];
[download]

open(I,$0);<I>;$~=$/;$/='~';$_=<I>;($/)=/(.)$~/;s/[$~~]//g;/(v)/;$-=$-[0];s;\Q$/\E;$~;g;($/,$^)=/^(.)(.)/;
#%  xxxxxx   xx-+  xx    xxx xx  xx       xx  xx   xxx   xxxxx+ xx  xx xxxx xxxxx  ......+
#x xxxxvxxx xx  xx xv   xxxx x+ %+  ===== xx  xx  xx xx  x+  =x xx xx  xx   xx xx ...+
#x xx xx xx xx  xx xx  xx xx xxx+         xxxxxx xx   +x xx     xx+x-  xxxx xxxx ........+
#% xx xx xx xx  xx xx xx  x+ xx xx  =+=== xx  xx xxxx-xx xx  =x +x xx  xx   xx xx ...+
#% xx xx xx  -+x+  xxx+   xx xx  xx       xx  xx x+   xx xxx+xx xx  xx xxxx xx  xx ....+~
for(split/$~/){s,[ $/],,g;/(.)$/;$l=$-[0];/(.)/||next;$_=chr$-+$l;$".=($1=~/$^/)?" \u$_":$_;}print$";