See JIRA ticket ENSCORESW-349

also save and restore operon_transcript_gene table
entries in the operon_transcript_gene table are not cleaned up

fix sent by mg13

updating the figure on how long it takes to run. The original estimate only took CPU time into account. This code does a lot in the DB so CPU usage is low

[ENSCORESW-335]. Allowed the input param force_species to populate species. Does using a hash. Higher up the levels we use a hash map plus decoding aliases so no need to worry about clashes between common and scientific names

[ENSCORESW-334]. EnsemblGenomes can also hand over species. Fixed the query to use an IN and bring EG in as well

commas though.

as first method has been removed in hive

always need to specify what type of object the attributes are being fetched for
use fetch_all_by_ method instead (fetch_all_by_Slice, fetch_all_by_Gene...)

allows to fetch all density features without for all slices
also takes an optional logic_name argument

for example fetch_all_by_Slice(slice) will return all seq_region_attrib for a given slice
now, fetch_all_by_Slice() will return all seq_region_attrib for all slices

Only use the coordinates with the smaller seq_region_id (usually 1-22,X,Y) to avoid mapping the LRG to the patch region