R/zzz.R

In HCBravoLab/silva128.1MgDb: SILVA SSR rRNA release 128.1 Annotation Data

###
### Load silva123.1MgDb into namespace
###

.onAttach <- function(libname, pkgname){

    db_file <- system.file("extdata", "silva128.1.sqlite",
                           package = pkgname, lib.loc = libname)

    tree_file <- system.file("extdata", "silva128.1.tre",
                             package = pkgname, lib.loc = libname)

    metadata_file <- system.file("extdata", "silva128.1_metadata.RDS",
                                 package = pkgname, lib.loc = libname)

    ## Note no tree for silva123.1

    if (!file.exists(db_file) | !file.exists(metadata_file)) {
        packageStartupMessage("SILVA 128.1 database data not present,
                              use `get_silva128.1.R` In the package
                              inst/scripts directory to download the
                              database into the package inst/extdata/
                              directory and reinstall the package")
    }
}

.onLoad <- function(libname, pkgname){
    ns <- asNamespace(pkgname)

    db_file <- system.file("extdata", "silva128.1.sqlite",
                                package = pkgname, lib.loc = libname)

    tree_file <- system.file("extdata", "silva128.1.tre",
                           package = pkgname, lib.loc = libname)

    metadata_file <- system.file("extdata", "silva128.1_metadata.RDS",
                                package = pkgname, lib.loc = libname)

    ## Add Tree data

    metadata <- readRDS(metadata_file)

    ## initiate new MgDB object
    slvMgDb <- metagenomeFeatures::newMgDb(db_file = db_file,
                      tree = tree_file,
                      metadata = metadata)

    assign("slv128.1MgDb", slvMgDb, envir = ns)
    namespaceExport(ns, "slv128.1MgDb")

    packageStartupMessage("Note that - there are 19,22,213 sequences in
            SILVA v.128 database, of which 29,467 sequences
            do not have RNACentral and NCBI taxon ID.")



}