GitLab

  Add missing ':' to 'RefSeq_dna:equus_caballus' in species section.

  Remove (comment out) non-existant source 'ncRNA::equus_caballus' from
  species section.


For pongo_pygmaeus:

  Replace non-existant source 'UniGene::pongo_pygmaeus' with
  'UniGene::MULTI' in species section.

Skip genes that are listed in Compara but aren't in the relevant core databases. Shouldn't be necessary in production runs but makes testing with previous Compara versions easier.

info for options added

default external_db_id to 11000 ('UCSC') manually.

Formatting.

Removed regulatory feature tables.

Added patch identifiers to meta table.

fetch_all_by_feature_class method now throws if there is an orphen analysis_id foreign key in the "feature_class" table

character limit on column 'attrib_type.code'.

they are.

  Type 75 (GeneNo_RNA_pseu):  Missing a tab character.

  Type 131 (vega_export_mode):  Type code changed to 'vega_export_mod'
  to conform to 15 character limit of column attrib_type.code.

from the list of tables to process.

  Remove hard-coded external_db_id 11000.

  Change xref.info_type from 'MISC' to 'COORDINATE_OVERLAP'.