#!/usr/bin/perl
my @data;
while (<DATA>) {
  chomp;
  push @data,[split /,/];
}

for my $z ( 0 .. $#data ) {
    for my $v ( 0 .. $#{$data[$z]} ) {
	print "$data[$v][$z],";
	}
    print "\n";
}

__DATA__
Date,a,b,c,d,e,f
Mon-1,11,12,13,14,15,16
Mon-2,21,22,23,24,25,26
Tue-1,31,,33,34,35,36
Tue-2,41,42,,44,45,46
Wed-1,51,52,53,54,55,56
Wed-2,61,62,63,64,65,66

##</code><code>##

May-1,May-2,May-3,May-.......,May-30
/dir/dir1/file1,3,34,,,,34,.......
/dir/dir1/dir3,.....
/dir/dir1/file2,....
/dir/dir1/file3,...
/dir/dir1/dir2....
..up to 1000-2000 rows..