In terms of how to get flat-file data into table, just read about "LOAD DATA INFILE" and "mysqlimport" in the mysql manual -- it's pretty clear and simple (a lot less hassle than the bulk-loader tools of some other RDB engines).
As for getting your perl script to write a flat file instead of doing inserts directly to mysql, just open an output file instead of a connection to the db. (Well, if some of your input is coming from the db, you can either connect to do the query, or save the query output to a file before running this script.)
When you get to the point in the script where you would have done an insert statement, just write those values to the output file as tab-delimited fields, terminated by a newliine. When done, close the file and use "system()" to run mysqlimport on it.
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