inst/extdata/GentlemanLab/generateSchemas.R

In Bioconductor/AnnotationForge: Tools for building SQLite-based annotation data packages

##Optional- depends on circumstances
##Get the latest (this step is slow)
##1st make sure that we have the latest packages installed
##(after they have been pushed)


##TO UPDATE: just go to the directory meant to hold the new schemas (be sure
##that you set it up in the DBs ahead of the change!) and then run this script
##from there.


##Need to put the packages in the latest AnnotationDbi schemas directory
##(source)
## schemaDir = "/mnt/cpb_anno/mcarlson/proj/mcarlson/AnnMod/AnnotationDbi/inst/DBschemas/schemas_2.0/"

##Now generate the schemas
library(AnnotationDbi)
library(DBI)
library(RSQLite)


pkgs = c(
  "GO_DB" = "GO.db", 
  "KEGG_DB" = "KEGG.db", 
  "PFAM_DB" = "PFAM.db",
  "INPARANOID_DB" = "hom.Hs.inp.db",
  "COELICOLOR_DB" = "org.Sco.eg.db",
  "ANOPHELES_DB" = "org.Ag.eg.db", 
  "ARABIDOPSIS_DB" = "org.At.tair.db", 
  "BOVINE_DB" = "org.Bt.eg.db", 
  "CANINE_DB" = "org.Cf.eg.db", 
  "CHICKEN_DB" = "org.Gg.eg.db", 
  "CHIMP_DB" = "org.Pt.eg.db", 
  "ECOLI_DB" = "org.EcK12.eg.db", 
  "FLY_DB" = "org.Dm.eg.db", 
  "HUMAN_DB" = "org.Hs.eg.db",  
  "MALARIA_DB" = "org.Pf.plasmo.db", 
  "MOUSE_DB" = "org.Mm.eg.db", 
  "PIG_DB" = "org.Ss.eg.db", 
  "RAT_DB" = "org.Rn.eg.db", 
  "RHESUS_DB" = "org.Mmu.eg.db", 
  "WORM_DB" = "org.Ce.eg.db", 
  "XENOPUS_DB" = "org.Xl.eg.db", 
  "YEAST_DB" = "org.Sc.sgd.db", 
  ## "YEASTNCBI_DB" = "", 
  "ZEBRAFISH_DB" = "org.Dr.eg.db",
  "ARABIDOPSISCHIP_DB" = "ag.db", 
  "BOVINECHIP_DB" = "bovine.db", 
  "CANINECHIP_DB" = "canine.db", 
  "CHICKENCHIP_DB" = "chicken.db", 
  ## "ECOLICHIP_DB" = "", 
  "FLYCHIP_DB" = "drosgenome1.db", 
  "HUMANCHIP_DB" = "hgu95av2.db", 
  "MOUSECHIP_DB" = "mgu74a.db", 
  ## "PIGCHIP_DB" = "", 
  "RATCHIP_DB" = "rae230a.db", 
  "WORMCHIP_DB" = "celegans.db", 
  "XENOPUSCHIP_DB" = "xlaevis.db",  ##Have to repeat once its installed.
  "YEASTCHIP_DB" = "yeast2.db", 
  "ZEBRAFISHCHIP_DB" = "zebrafish.db")
  

for(i in seq_len(length(pkgs))){
    AnnotationDbi:::generate.schema(names(pkgs[i]),pkgs[i])
}