However, there are certain limits in MySQL (from the v.5.0 docs):
D.7.2. The Maximum Number of Columns Per Table
There is a hard limit of 4096 columns per table, but the effective maximum may be less for a given table. The exact limit depends on several interacting factors, listed in the following discussion.
Every table has a maximum row size of 65,535 bytes. This maximum applies to all storage engines, but a given engine might have additional constraints that result in a lower effective maximum row size.
The maximum row size constrains the number of columns because the total width of all columns cannot exceed this size. For example, utf8 characters require up to three bytes per character, so for a CHAR(255) CHARACTER SET utf8 column, the server must allocate 255 × 3 = 765 bytes per value. Consequently, a table cannot contain more than 65,535 / 765 = 85 such columns.
Will your transposed data fit within these limits?
Another very practical question: what will be the column-names? Is there a way to generate them automatically?
A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James