* Pick up perl executable from environment.

  * use warnings;

  * Make usage() a subroutine rather than a string.

  * Use @table_names in usage() to avoid confusion when the list of
    tables is updated (the 'ditag' table was missing from the list, but
    not in the old usage string).

  * Better usage() text.

  * Better information messages when running the script.

  * When unable to dump the old table, skip to the next database rather
    than dying.

  * Always use long option names when calling external programs from scripts!

  * Use do() rather than prepare(), execute(), finish() for simple
    things like these.

for port to '3306'. Some formatting.

Replacing the 6 coordinate methods with versions which can operate on transcripts which have not been persisted to a database. The DBID is still used for caching purposes

Switch to using $subsequence_slice than $self for the start and end values. If we don't then we will try to retrieve all repeat features for an entire chromosome.

Simplification of the AUTOLOAD since there were blocks of code which could never be called. Removed these unused blocks.