R/makeRepDbLitePkg.R

In arcolombo/TxDbLite: Lightweight SQLite-based annotation classes/packages for use with arkas

#' create a RepDbLite package from sqlite file (usually via repDbLiteFromFasta)
#'
#' @param repdblitefile   the sqlite filename
#' @param author          whose fault this is
#' @param email           email address 
#' @param version         version of the package (default is "1.0")
#' @param destDir         where to put the new package directory (".")
#' @param ...             additional parameters
#' @importFrom Biobase createPackage
#' @importFrom ensembldb metadata
#' @return the name of the package 
#' 
#' @export
makeRepDbLitePkg <- function(repdblitefile, author="Nobody", email="dev@null.com", version="1.0", destDir=".", ...) {
  
  stopifnot(class(repdblitefile) == "character")
  repdb <- RepDbLite(x=repdblitefile)
  md <- metadata(repdb)
  fetchMeta <- function(x) md[x, "value"]
  pkg <- fetchMeta("package_name")
  maintainer <- paste0(author, " <", email, ">")
  organism <- fetchMeta("organism")
  repbase_version <- as.character(fetchMeta("genome_build"))
  template_path <- system.file("repdblite", package="TxDbLite")
  source_url <- paste0("http://www.girinst.org/server/RepBase/protected/",
                       "RepBase", repbase_version, ".fasta/")
  release_date <- fetchMeta("creation_time")
  symvals <- list(
    PKGTITLE="RepBase-based annotation package",
    PKGDESCRIPTION="lightweight RepBase transcript annotations",
    PKGVERSION=version,
    AUTHOR=author,
    MAINTAINER=maintainer,
    LIC="Artistic-2.0",
    ORGANISM=organism, 
    SPECIES=organism, 
    PROVIDER="RepBase",
    PROVIDERVERSION=repbase_version,
    RELEASEDATE=release_date,
    SOURCEURL=source_url,
    ORGANISMBIOCVIEW=gsub(" ","_", organism), 
    TXDBOBJNAME=pkg
  )


  createPackage(pkgname=pkg,
                destinationDir=destDir,
                originDir=template_path,
                symbolValues=symvals,
                ...)
  dir.create(paste(c(destDir, pkg, "inst", "extdata"), 
                   collapse=.Platform$file.sep),
             showWarnings=FALSE, recursive=TRUE)
  db_path <- file.path(destDir, pkg, "inst", "extdata", repdblitefile)
  file.copy(repdblitefile, to=db_path)
  return(pkg)

}