Attempting to fix the issues with too many KNOWN status genes appearing in species we should not be seeing them in. UniProtParser now limits to using ACs with an evidence of 1 and 2. We now do not assign KNOWN based upon a depdendent xref when we didn't trust the parent xref. Also the loader & SQL has been edited to allow for LOWEVIDENCE types of sources.

Added RNAMMEr and TRANSCAN_SE to the list of sources for gene descriptions; added a method called set_source_id_to_external_name

automatic and curated version of HGNC and MGI have now been removed. Also display_xref+id is set in the official naming routine

allow user to set a list of sources that will not have the [Source:...] bit at the end of the gene description

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

a) added unused_priority to the order list as this now contains the number of times that trancript name was used and is need to make sure that the gene name is the same as the transcripts. b) make sure there is a description else we get a ton of warning regarding undefined vars

if noxref_database is specified do not try to write to the xref database. Needed for -recalc_display_xrefs option

Get the sources to be used for display_xrefs and gene decriptions from the species file if it exists

new test code to calculate display xrefs using the xref database and SQL only. So much, much faster as just simple sql instead of gettin gall genes, then all transcripts then all dbentries. Caveat though is that all the xrefs have to be in the xref database and cannot be used to an update mode. i.e. just adding one particular source.  Can only be used whan adding ALL sources possible.