Raw content of EnsEMBL::Ensembl::SiteDefs package EnsEMBL::Ensembl::SiteDefs; use strict; sub update_conf { $SiteDefs::ENSEMBL_PRIMARY_SPECIES = 'Homo_sapiens'; # Default species $SiteDefs::ENSEMBL_SECONDARY_SPECIES = 'Mus_musculus'; # Secondary species ## This hash is used to configure the species available in this ## copy of EnsEMBL - comment out any lines which are not relevant ## If you add a new species MAKE sure that one of the values of the ## array is the "SPECIES_CODE" defined in the species.ini file #-------------------- mammals $SiteDefs::__species_aliases{ 'Bos_taurus' } = [qw(bt btau cow moo)]; $SiteDefs::__species_aliases{ 'Canis_familiaris' } = [qw(cf cfam dog)]; $SiteDefs::__species_aliases{ 'Cavia_porcellus' } = [qw(cp cpor guineapig)]; $SiteDefs::__species_aliases{ 'Choloepus_hoffmanni' } = [qw(ch chof sloth)]; $SiteDefs::__species_aliases{ 'Dasypus_novemcinctus' } = [qw(dn dnov dasypus armadillo)]; $SiteDefs::__species_aliases{ 'Dipodomys_ordii' } = [qw(do kangaroorat)]; $SiteDefs::__species_aliases{ 'Echinops_telfairi' } = [qw(et etel echinops tenrec)]; $SiteDefs::__species_aliases{ 'Equus_caballus' } = [qw(ec horse)]; $SiteDefs::__species_aliases{ 'Erinaceus_europaeus' } = [qw(ee eeur hedgehog)]; $SiteDefs::__species_aliases{ 'Gorilla_gorilla' } = [qw(ggo kong gorilla)]; $SiteDefs::__species_aliases{ 'Felis_catus' } = [qw(fc fcat cat)]; $SiteDefs::__species_aliases{ 'Gorilla_gorilla' } = [qw(gg ggor gorilla kong)]; $SiteDefs::__species_aliases{ 'Homo_sapiens' } = [qw(hs hsap human man default)]; $SiteDefs::__species_aliases{ 'Loxodonta_africana' } = [qw(la lafr elephant africana loxodontai hathi nellie dumbo)]; $SiteDefs::__species_aliases{ 'Oryctolagus_cuniculus' } = [qw(oc ocun rabbit bugs bunny hutch harvey)]; $SiteDefs::__species_aliases{ 'Macaca_mulatta' } = [qw(mmu mmul rhesus macaque macaca)]; $SiteDefs::__species_aliases{ 'Microcebus_murinus' } = [qw(mmur lemur)]; $SiteDefs::__species_aliases{ 'Monodelphis_domestica' } = [qw(md mdom monodelphis opossum)]; $SiteDefs::__species_aliases{ 'Mus_musculus' } = [qw(mm mmus mouse mus)]; $SiteDefs::__species_aliases{ 'Myotis_lucifugus' } = [qw(ml mluc microbat myotis)]; $SiteDefs::__species_aliases{ 'Ochotona_princeps' } = [qw(op pika pikachu)]; $SiteDefs::__species_aliases{ 'Ornithorhynchus_anatinus' } = [qw(oa oana platypus)]; $SiteDefs::__species_aliases{ 'Otolemur_garnettii' } = [qw(og ogar bushbaby otolemur)]; $SiteDefs::__species_aliases{ 'Pan_troglodytes' } = [qw(pt ptro chimp)]; $SiteDefs::__species_aliases{ 'Pongo_pygmaeus' } = [qw(pp orang orangutan librarian ook)]; $SiteDefs::__species_aliases{ 'Procavia_capensis' } = [qw(pc hyrax dassy dassie pimbi)]; $SiteDefs::__species_aliases{ 'Pteropus_vampyrus' } = [qw(pv megabat flyingfox)]; $SiteDefs::__species_aliases{ 'Rattus_norvegicus' } = [qw(rn rnor rat)]; $SiteDefs::__species_aliases{ 'Sorex_araneus' } = [qw(sa shrew)]; $SiteDefs::__species_aliases{ 'Spermophilus_tridecemlineatus' } = [qw(st stri squirrel spermophilus)]; $SiteDefs::__species_aliases{ 'Tarsius_syrichta' } = [qw(ts tarsier gremlin)]; $SiteDefs::__species_aliases{ 'Tupaia_belangeri' } = [qw(tb tbel treeshrew shrew)]; $SiteDefs::__species_aliases{ 'Tursiops_truncatus' } = [qw(tt dolphin flipper)]; $SiteDefs::__species_aliases{ 'Vicugna_pacos' } = [qw(lp alpaca)]; #-------------------- birds $SiteDefs::__species_aliases{ 'Gallus_gallus' } = [qw(gg ggal chicken)]; $SiteDefs::__species_aliases{ 'Taeniopygia_guttata' } = [qw(tg taegut taeniopygia zebrafinch)]; #-------------------- fish $SiteDefs::__species_aliases{ 'Danio_rerio' } = [qw(dr drer zfish zebrafish)]; $SiteDefs::__species_aliases{ 'Gasterosteus_aculeatus' } = [qw(ga gacu stickleback gasterosteus)]; $SiteDefs::__species_aliases{ 'Oryzias_latipes' } = [qw(ol olat medaka)]; $SiteDefs::__species_aliases{ 'Takifugu_rubripes' } = [qw(fr trub ffish fugu takifugu f_rubripes fugu_rubripes)]; $SiteDefs::__species_aliases{ 'Tetraodon_nigroviridis' } = [qw(tn tnig tetraodon)]; #-------------------- amphibians $SiteDefs::__species_aliases{ 'Xenopus_tropicalis' } = [qw(xt xtro xenopus frog)]; #-------------------- reptiles $SiteDefs::__species_aliases{ 'Anolis_carolinensis' } = [qw(ac anolis anole lizard)]; #-------------------- flies $SiteDefs::__species_aliases{ 'Aedes_aegypti' } = [qw(aa aaeg aedes )]; $SiteDefs::__species_aliases{ 'Anopheles_gambiae' } = [qw(ag agam mosquito mos anopheles)]; # $SiteDefs::__species_aliases{ 'Apis_mellifera' } = [qw(am amel honeybee bee)]; $SiteDefs::__species_aliases{ 'Drosophila_melanogaster' } = [qw(dm dmel fly)]; #-------------------- worms # $SiteDefs::__species_aliases{ 'Caenorhabditis_briggsae' } = [qw(cb cbri briggsae)]; $SiteDefs::__species_aliases{ 'Caenorhabditis_elegans' } = [qw(ce cele worm elegans)]; $SiteDefs::__species_aliases{ 'Ciona_intestinalis' } = [qw(ci cint seasquirti cionai)]; $SiteDefs::__species_aliases{ 'Ciona_savignyi' } = [qw(cs csav seasquirts cionas)]; #-------------------- yeast $SiteDefs::__species_aliases{ 'Saccharomyces_cerevisiae' } = [qw(sc scer yeast saccharomyces )]; } 1;