ALTER [IGNORE] TABLE will ignore certain errors, such as duplicating key errors when adding a new UNIQUE index or errors in SQL mode.
http://dev.mysql.com/doc/refman/4.1/en/alter-table.html
More information about the "script" you are using will help answer the question. For example, in python, an error would throw an exception, which could then be caught, processed, or ignored.
[EDIT] From the comment below, it seems that you are looking for the mysql -f command line option.
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