/usr/lib/R/site-library/GenomicFeatures/script/maketRNAFDb.R is in r-bioc-genomicfeatures 1.30.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | ## It all has to start with an FDB package
library(GenomicFeatures)
makeFDbPackageFromUCSC(version="1.0.0",
maintainer="Bioconductor Package Maintainer <maintainer@bioconductor.org>",
author="Marc Carlson",
genome="hg19",
track="tRNAs",
tablename="tRNAs")
## Now I must make more FBDs and save their SQLite files to this package
path <- "FDb.Hsapiens.UCSC.hg19.tRNAs/inst/extdata/"
species <- c(hg18 = "Hsapiens",
mm9 = "Mmusculus",
mm10 = "Mmusculus",
rn4 = "Rnorvegicus",
rn5 = "Rnorvegicus")
for(i in seq_len(length(species))){
fdb <- makeFeatureDbFromUCSC(genome=names(species[i]),
track="tRNAs",
tablename="tRNAs")
name <- paste("FDb.",species[i],".UCSC.",names(species[i]),
".tRNAs.sqlite",sep="")
saveDb(fdb, file=paste(path,name,sep=""))
}
################################################################################
## Then change what we call it:
file.rename("FDb.Hsapiens.UCSC.hg19.tRNAs","FDb.UCSC.tRNAs")
## Then rename it in DESCRIPTION
fl <- file("FDb.UCSC.tRNAs/DESCRIPTION")
lns <- readLines(fl)
lns <- gsub("FDb.Hsapiens.UCSC.hg19.tRNAs","FDb.UCSC.tRNAs",lns)
writeLines(lns, con = fl)
## Make some edits to the manual page
fl <- file("FDb.UCSC.tRNAs/man/package.Rd")
lns <- readLines(fl)
lns <- gsub("FDb.Hsapiens.UCSC.hg19.tRNAs","FDb.UCSC.tRNAs",lns)
## except for the last one which should always be on line 41
lns[[41]] <- sub("FDb.UCSC.tRNAs","FDb.Hsapiens.UCSC.hg19.tRNAs",lns[[41]])
lns <- c(lns[1:8],
"\\alias{FDb.Hsapiens.UCSC.hg19.tRNAs}",
"\\alias{FDb.Hsapiens.UCSC.hg18.tRNAs}",
"\\alias{FDb.Mmusculus.UCSC.mm9.tRNAs}",
"\\alias{FDb.Mmusculus.UCSC.mm10.tRNAs}",
"\\alias{FDb.Rnorvegicus.UCSC.rn4.tRNAs}",
"\\alias{FDb.Rnorvegicus.UCSC.rn5.tRNAs}",
lns[9:length(lns)])
writeLines(lns, con = fl)
## OLDE Stuff follows:
## FDb..UCSC..tRNAs <- makeFeatureDbFromUCSC(genome="",
## track="tRNAs",
## tablename="tRNAs")
## save(, file=paste(path,".sqlite",sep=""))
## FDb.Hsapiens.UCSC.hg18.tRNAs <- makeFeatureDbFromUCSC(genome="hg18",
## track="tRNAs",
## tablename="tRNAs")
## saveDb(FDb.Hsapiens.UCSC.hg18.tRNAs,
## file=paste(path,"FDb.Hsapiens.UCSC.hg18.tRNAs.sqlite",sep=""))
## FDb.Mmusculus.UCSC.mm9.tRNAs <- makeFeatureDbFromUCSC(genome="mm9",
## track="tRNAs",
## tablename="tRNAs")
## saveDb(FDb.Mmusculus.UCSC.mm9.tRNAs,
## file=paste(path,"FDb.Mmusculus.UCSC.mm9.tRNAs.sqlite",sep=""))
## FDb.Rnorvegicus.UCSC.mm9.tRNAs <- makeFeatureDbFromUCSC(genome="rn4",
## track="tRNAs",
## tablename="tRNAs")
## saveDb(FDb.Rnorvegicus.UCSC.mm9.tRNAs,
## file=paste(path,"FDb.Rnorvegicus.UCSC.mm9.tRNAs.sqlite",sep=""))
################################################################################
## And then I have to totally change the way the /R/zzz.R looks - vectorized
## for all.
## Should look more like this
## .onLoad <- function(libname, pkgname)
## {
## ns <- asNamespace(pkgname)
## path <- system.file("extdata", package=pkgname, lib.loc=libname)
## files <- dir(path)
## for(i in seq_len(length(files))){
## fdb <- loadDb(system.file("extdata", files[[i]], package=pkgname,
## lib.loc=libname),packageName=pkgname)
## objname <- sub(".sqlite$","",files[[i]])
## assign(objname, fdb, envir=ns)
## namespaceExport(ns, objname)
## }
## }
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