Program is now executable and also attempts to diagnose the issues a user can face when setting up the API.

Adding in methods to retrieve repeat types from repeat_consensus. Also increased the number of types we can limit by at once

Applying a fix for when the schema patcher is run from the misc-scripts directory and now default it to the current directory if no directory is extracted from __FILE__. We also have improved the warning about missing directories

Changes to allow for a global path setting to be given as well as delegating to the meta table. Also made the data_file be able to hand back the external data adaptor

Bugfix for issue raised by Michael Nuhn from Ensembl Genomes. fetch_all_by_Transcript_list() incorrectly assigned the canonical translation ID

Pushing in a non-interactive mode. Important since some people are happy to do dry runs & then apply

Patched to compute the location of the directory from the schema patcher file location and not assuming a user will execute this script from the misc-scripts directory. This reduces the need to use --cvsdir so much. We also do some sanity checking to make sure we can find the schema file in the directory which reports to be the SQL dir

Introduction of new FASTASerializer to replace SeqDumper's FASTA capability. Other formats remain SeqDumper's responsibility.

Few updates. If a db has been replaced by a later assembly the script will do an update not an insert. We also remove the databases from the db table which are no longer active but only after a user confirms it