Currently I run an 'updater' script to run through a directory of .sql files
using something like this in PHP:

        $COMMAND = "mysql ".$OPTION['db_prefix'].$db." < ".$mydir.$filename;
        system($COMMAND, $ret);

What would be the equivallent way to to this in a PHP mysql_query(""); way?

I see "LOAD", but that only works for data it seems.
http://dev.mysql.com/doc/refman/5.0/en/load-data.html

These scripts I use have ALTER statements and CREATE and all other types of
SQL in them and almost no data actually.

mySQL 5.0.15


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