processed_transcript', if gene biotype is protein_coding.

The TranslationAdaptor now has a fetch_all_by_Transcript() method with
which it's possible to get all translations for a transcript.

The fetch_by_Transcript() method now uses the new
canonical_translation_id field in the transcript table to get the
canonical transcript.

For species without alternative initiation (all Core speaces today), the
semantics and the results are the same as before.

Using the API from now on, without patch_56_57_e.sql applied, will
result in SQL errors.

The TranscriptAdaptor now knows how to store the canonical translation ID.

results anyway).

command line arguments standardized to the ones used in the genebuild scripts ( dbhost dbname dbport ... )

warnings when the port is an empty string.

the stable ID mapping scripts.  Fixes breakage for human.

#
# Title: Expand width of simple_feature.display_label

Expands width of simple_feature.display_label to 128.

Do not repair automatically.
Add informationl blurb at end of execution.

comparing them betwixt source and target database.

does not follow the simple "table_name.{MYI,MYD}" naming scheme.  Make
the script properly handle these anyway.