R/getMetaGenomeAnnotations.R

In HajkD/biomartr: Genomic Data Retrieval

#' @title Retrieve annotation *.gff files for metagenomes from NCBI Genbank
#' @description Retrieve available annotation *.gff files for metagenomes 
#' from NCBI Genbank. NCBI Genbank allows users
#' to download entire metagenomes and their annotations of several metagenome 
#' projects. This function downloads available metagenomes that can then be 
#' downloaded via \code{\link{getMetaGenomes}}.
#' @param name metagenome name retrieved by \code{\link{listMetaGenomes}}.
#' @param path a character string specifying the location (a folder) 
#' in which the corresponding metagenome annotations shall be stored. 
#' Default is
#' \code{path} = \code{file.path("_ncbi_downloads","metagenome","annotations")}.
#' @author Hajk-Georg Drost
#' @examples
#' \dontrun{
#' # Frist, retrieve a list of available metagenomes
#' listMetaGenomes()
#'
#' # Now, retrieve the 'human gut metagenome'
#' getMetaGenomeAnnotations(name = "human gut metagenome")
#' }
#' @seealso \code{\link{getMetaGenomes}}, \code{\link{listMetaGenomes}}, 
#' \code{\link{getGFF}}  
#' @export

getMetaGenomeAnnotations <-
    function(name,
             path = file.path("_ncbi_downloads", "metagenome", "annotations")) {
        if (!is.element(name, listMetaGenomes(details = FALSE)))
            stop(
                paste0("Unfortunately, the metagenome '",
                name,
                "' is not available. Please consult the listMetaGenomes() ",
                "function for available metagenomes.")
            )
        
        if (!file.exists(path)) {
            dir.create(path, recursive = TRUE)
        }
        
        organism_name <- NULL
        
        # retrieve metagenomes assembly_summary.txt file
        mgs <- getMetaGenomeSummary()
        
        metagenomes.members <-
            dplyr::filter(mgs, organism_name == name)
        file.names <- metagenomes.members$ftp_path
        
        for (i in seq_len(length(file.names))) {
            download_url <-
                paste0(
                    file.names[i],
                    "/",
                    paste0(
                        metagenomes.members$assembly_accession[i],
                        "_",
                        metagenomes.members$asm_name[i],
                        "_genomic.gff.gz"
                    )
                )
            
            tryCatch({
                utils::capture.output(downloader::download(
                    download_url,
                    destfile = file.path(path, paste0(
                        basename(file.names[i]), "_genomic.gff.gz"
                    )),
                    mode = "wb"
                ))
            }, error = function(e)
                message(
                    "Unfortunately, the FTP site 'ftp://ftp.ncbi.nlm.nih.gov/' cannot be 
                    reached. This might be due to an instable internet connection or some issues with the firewall.  
                     Are you able to reach the FTP site '",
                    download_url,
                    "' from your browser?"
                ))
            
            docFile(
                file.name = paste0(basename(file.names[i]), "_genomic.gff.gz"),
                organism  = basename(file.names[i]),
                url       = download_url,
                database  = "Genbank metagenomes",
                path      = path,
                refseq_category = metagenomes.members$refseq_category[i],
                assembly_accession = metagenomes.members$assembly_accession[i],
                bioproject = metagenomes.members$bioproject[i],
                biosample = metagenomes.members$biosample[i],
                taxid = metagenomes.members$taxid[i],
                infraspecific_name = metagenomes.members$infraspecific_name[i],
                version_status = metagenomes.members$version_status[i],
                release_type = metagenomes.members$release_type[i],
                genome_rep = metagenomes.members$genome_rep[i],
                seq_rel_date = metagenomes.members$seq_rel_date[i],
                submitter = metagenomes.members$submitter[i]
            )
        }
        
        print(
            paste0(
                "The annotations of metagenome '",
                name,
                "' have been downloaded and stored at '",
                path,
                "'."
            )
        )
        
        file.paths <- file.path(path, list.files(path = path))
        # return only file paths without "*.txt"
        return(file.paths[!unlist(lapply(file.paths, function(x)
            stringr::str_detect(x, "[.]txt")))])
}