#' @title Retrieve All Organism Names Stored on refseq
#' @description This function extracts all organism names (scientific names)
#' for which genomes, proteomes, and CDS files are stored on
#' the NCBI refseq server.
#' @author Hajk-Georg Drost
#' @export
refseqOrganisms <- function() {
refseq_kingdoms <- c(
"archaea",
"bacteria",
"fungi",
"invertebrate",
"plant",
"protozoa",
"vertebrate_mammalian",
"vertebrate_other"
)
all_refseqOrgs <-
as.vector(unlist(lapply(refseq_kingdoms, function(kingdom)
strsplit(
RCurl::getURL(
paste0(
"ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/",
kingdom,
"/"
),
ftp.use.epsv = FALSE,
dirlistonly = TRUE
),
"\n"
))))
all_refseqOrgs <-
stringr::str_replace(all_refseqOrgs, "_", " ")
return(all_refseqOrgs)
}
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