I guess I found what I was doing wrong.(why it gave me garbled text when decoding cp1254 encoded data with iso-8859-9)

It could be useful for other people in the future. (It's a silly mistake though)

I was opening the file with this argument

open FILE, "+<file.txt";

I load the file content into a variable as I said before. (I need to do that in order to update the row) After I decode the data, I was writing the decoded data into the same file. So the encoding stays same actually on that file. We need to delete the file and create new one. That's the problem.

(or we can use something like iconv, but it won't make any difference I guess, since we need to load the data into a variable to determine its encoding and update the databasae)

Thanks again,