A simple python program would do the job (and since this is not really tested: backup you csv file in advance!):

import csv

import sys

infile = sys.argv[1]

outfile = sys.argv[2]



with open(infile) as f:

    reader = csv.reader(f)

    cols = []

    for row in reader:

        cols.append(row)



with open(outfile, 'wb') as f:

    writer = csv.writer(f)

    for i in range(len(max(cols, key=len))):

        writer.writerow([(c[i] if i<len(c) else '') for c in cols])

You can save this into a file "my_csv_transposer.py" and call it from the commandline like this:

python my_csv_transposer.py <theinfilename> <theoutfilename>