when projecting a symbol onto a gene, use the same symbol for all attached transcripts, with version number in format -201
for all species now, not just pig

Added GOA webservice call, timeout response, and subsequent usage of the blacklist to the projections.

Pushing pig specific hacks for the naming of transcripts and the overwriting of xref pipeline assigned values (in a similar way we do for zfish)

Allowing backups to go to a directory other than our current working directory. Can cause some issues with disk quotas

Fixed an inappropriate method of getting species aliases and changed a couple of lines to be more direct.

First draft of revised projections. Exclusions in place for inappropriate mammalian traits on birds and reptiles. Also platypus.

Awaiting GOA full blacklist of undesirable projections.

Replaced RefSeq_dna_predicted with Refseq_mRNA_predicted and RefSeq_ncRNA_predicted as the RefSeq_dna_predicted have been split for release 64.

Force the loading of external synonyms before getting the code to store them. Otherwise we incorrectly retrieve external synonyms from the source database with a newly assigned ID

for multiple gene numbers the zebrafish naming need to use the original name and not the modified one in future gene numbers.

Added code to fix issue with Corf genes in zebrafish. The gene names were not being modified to look like hsC*orf*-like. This now works.

Add projected xrefs to genes rather than transcripts by default if there is no equivalent type in the target database.

Added code to delete names/GO terms if the -delete_only option is specified. Added code to check whether
-registryconf is submitted as a string from the submit_projections.pl script or as a file on the command
line.

Use the translations of the _canonical_ transcripts of the source and target genes as the source of GO terms to project, rather than simply the longest translation in each, which was a bit arbitrary and didn't alway work.

Also make the print option for GO term projection a bit more verbose - aids debugging.

Skip projection of genes from sources with "clone" in the db name - should stop mouse clone names being projected to rat & kangaroo rat.

Set gene description to NULL and status back to KNOWN_BY_PROJECTION when deleting previously-projected xrefs.