Here is an oldie but a goodie from Tachyon. Just have a data file called data.txt in the dir, and it will transpose it. It looks for strings separated by spaces, but you should be able to modify it to use with commas.(Or modify your data)

#!/usr/bin/perl
# maybe look at  Math::Matrix

# by Tachyon
# The main requirement is that you have as much free disk space 
# for the temp files as the total file size. You will be limited 
# in the number of columns you can transpose by the number of open 
# file descriptors your Perl will let you have. It is very easy to 
# hack the logic to do N colunms per pass at the expense of 1 full 
# read of the input file per extra pass. Alternatively you could DBM 
# or tie a hash to a file and use the keys as pseudo file handles 
# and just append data to the values.

# It should be really fast as we make a single pass through the input 
# data and then effectively just write it out (each temp file has one 
# full line in it).
# transpose.pl

#works but the temp files seems wasteful to me

use strict;
transpose90( "data.txt", "data-transpose.txt" );

sub transpose90 {
    my ( $infile, $outfile, $tmp ) = @_;
    $tmp ||= 'temp';
    open IN, $infile or die "Can't read $infile $!\n";
    # find number of columns and open a temp file for each
    local $_ = <IN>;
    chomp;
    my @data = split ' ';
    my $num_cols = $#data;
    my @fhs;
    open $fhs[$_], ">$tmp$_.txt" or die "Can't create temp file $tmp$_
+ $!\n"
        for 0..$num_cols;
    print {$fhs[$_]} $data[$_], "\t" for 0..$num_cols;
    while( <IN> ) {
        chomp;
        @data = split ' ';
        print {$fhs[$_]} $data[$_], "\t" for 0..$num_cols;
    }
    close IN;
    close $fhs[$_] for 0..$num_cols;
    open OUT, ">$outfile" or die "Can't write $outfile $!\n";
    for ( 0.. $num_cols ) {
        open IN, "$tmp$_.txt" or die "Can't read temp file $tmp$_ $!\n
+";
        print OUT scalar(<IN>), "\n";
        close IN;
        unlink "$tmp$_.txt"
    }
    close OUT;
}
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