GitLab

species and group deprecatied. As these should not be used now that dbc is not part of the dbadaptor anymore.

Bug fix correcting sorting of transcript display_xrefs (originally between v1.83-1.84) had been reverted somehow. Re-instated.

subroutine clear, now added which will drop all database connections and reset the registry.  NOTE: if you load_all and the registry is loaded the subroutine clear is now automatically called first to clear out the old configuration before loading the new one.

Updated ith new linkable, priority columns. Also added cdna to list of database types and removed estgene.

ZFINParser.pm now actually stores Xrefs. Modified GOParser.pm to handle ZFIN.

option -drop_db from xref_parser.pl implemented which prevents the 'yes' command (scripting and logging purposes )

option -dropdb || -drop_db added to create new xref-db without having to enter 'yes' (scripting purposes )

small change to allow both Wills and thepipeline method of storing markers to work

made all registry calls case INsensetive as it was very annoying having to have species, group and type all in the correct case. Also added load_registry_from_db which will load the latest ensembl databases given a database host (and optionally port, user, pass) to search. At prsent only core,variation,estgene,compara and go adaptors are loaded via this method.

ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/7227.spc

===========>

       ftp://ftp.ebi.ac.uk/pub/databases/integr8/17.D_melanogaster.dat.gz

and invertebrate9.protein.gpff.gz added

get_all_homologous_Genes method catches the exception when calling get_Gene from a compara member object.