#' create an annotation package for a FASTA file (try to figure out what kind)
#'
#' @param fastaFile the filename
#' @param ... additional arguments related to package creation.
#' @return the name of the annotation package, or NULL if uncertain how to do it
#'
#' @import Biobase
#' @import DBI
#' @import RSQLite
#'
#' @export
createAnnotationPackage <- function(fastaFile, ...) { # {{{
type <- getAnnotationType(fastaFile)
if (is.null(type)) {
message("Couldn't find a known type for ", fastaFile, ", skipping...")
return(NULL)
} else if (type == "EnsDbLite") {
db <- ensDbLiteFromFasta(fastaFile)
pkg <- makeEnsDbLitePkg(db, ...)
} else if (type == "RepDbLite") {
db <- repDbLiteFromFasta(fastaFile)
pkg <- makeRepDbLitePkg(db, ...)
#} else if (type == "MitxDbLite") {
# db <- mitxDbLiteFromFasta(fastaFile)
# pkg <- makeMitxDbLitePkg(db, ...)
} else if (grepl("ERCC", fastaFile)) {
db <- erccDbLiteFromFasta(fastaFile)
pkg <- makeErccDbLitePkg(db, ...)
} else {
message("Don't know how to annotate ", fastaFile, ", skipping...")
return(NULL)
}
# FIXME: so ghetto it hurts
cmd <- paste("R CMD INSTALL", pkg)
system(cmd)
return(pkg)
} # }}}
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