The MySmartUSB documentation contains a paragraph about a protocol for sending commands to the programmer. I wrote a small perl script that can send these commands.
The file: mysmartusb. It requires Device::SerialPort, which is a perl module that's available on CPAN.
Or you could get the git repository from http://code.peterstuifzand.nl/git/mysmartusb.git with the command:
git clone http://code.peterstuifzand.nl/git/mysmartusb.git/