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.

added support for different cache methods (currently implemented: build_cache_all() and build_cache_by_seq_region()

methods for initial db checks; two variants of build_cache(): build_cache_by_seq_region() and build_cache_all()

1)  Indicate truncated Xref descriptions by appending ' /.../' to
    the end of them.  The maximum length of the descriptions is 255
    characters (including this truncation marker).

2)  Properly check for successful running of the 'xref_config2sql.pl'
    script and be verbose about reporting failures (from the
    documentation of the 'system' command).