* 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.