Added OTTG and change the codes to be 4600, 4610 ad 4620 corresponding to gene, transcript and translation to be consistent with other similar types

Added OTTG and change the codes to be 4600, 4610 ad 4620 corresponding to gene, transcript and translation to be consistent with other similar types

Added OTTG and change the codes to be 4600, 4610 ad 4620 corresponding to gene, transcript and translation to be consistent with other similar types

Swap order of name,coord_system ID in seq_region unique index, and add new index on coord_system ID. Remove redundant name index.

ANALYSE TABLE is run after the index modifications, so this patch may take a few minutes to execute.

Change gene.canonical_transcript to canonical_transcript_id, and add canonical_annotation, DEFAULT NULL

Added hcoverage to pep_check_sql and dna_check_sql. Also added hcoverage to @check_args so that hcoverage is checked when looking at what has already been written.

of the feature table are first and in the order thay are defined in the
SQL schema.

RepeatFeature.

process the first 100 of them.

Slightly more elegant way of collecting results in
_type_by_external_id() and in _type_by_external_db_id().

2048 in fetch_all_by_dbID_list():

  # Ensure that we do not exceed MySQL's max_allowed_packet (defaults to
  # 1 MB) splitting large queries into smaller queries of at most 256 KB
  # (32768 8-bit characters).  Assuming a (generous) average dbID string
  # length of 16, this means 2048 dbIDs in each query.

The observed decrease in time for unsorted dbID lists of 10000 IDs
ranged between 5% to just under 10% depending on feature type, lower
(around 3%) for sorted ID lists.

Some reformatting.

(MySQL v5 knows how to do index merges) in _type_by_external_id():

  # decrease in time by 35%
  $dbea->list_transcript_ids_by_extids('BRCA2');

  # decrease in time by 28%
  $dbea->list_translation_ids_by_extids('GO:0004835');

  # decrease in time by 24%
  $dbea->list_gene_ids_by_extids('ARSE');


Also some formatting.

got rid of a bad line

extras for tetraodon

in human is number 118 in length, no gene, %gc, or SNP density features
were being calculated for it.