added support for fetching somatic mutations from a slice, and tidied up the general variation feature fetching code

Pointed out by Andy Yates.

reset staus for genes and transcripts to those from havana if ALL transcripts for a gene and the gene itself have a valid status in havana

change to using registry so that we do not have to specify the release number. That way we do not have to change the config file for every release

  get_production_name()
  get_short_name()
  get_common_name()
  get_scientific_name()

These will return the corresponding meta values (for keys
'species.common_name' etc.) once these have been inserted
in the Core databases (during the release process of 59).

Details:
http://www.ebi.ac.uk/seqdb/confluence/display/EnsGen/Meta+Changes+for+59+and+release+6

into account.

table.

changed parsers as curated_trascriptParserhas now replaced HGNC_curated_transcriptParser and MGI_curated_transcriptParser

curated_transcriptParser now replaces HGNC and MGI variants as it was basically the same code in both

Added Aspergillus_fumigatus A1163 species, updated niger species entry, added SGD_GENE and SGD_TRANSCRIPT sources