get.supplied.comparison.template.path.virus <- function(virus, region) {
if (length(region) == 0 || region == "") {
return(NULL)
}
path <- system.file("extdata", "Vir", virus, region, "comparison",
"templates", package = "openPrimeR")
csv.file <- list.files(path, full.names = TRUE)[1]
if (!file.exists(csv.file)) {
warning(paste0("Template comparison data for ", virus, " and ", region,
",not found!"))
return(NULL)
}
res <- list(datapath = csv.file, name = region)
return(res)
}
get.available.viruses <- function() {
# determine for which viruses there are available template sequences
virus.folder <- system.file("extdata", "Vir", package = "openPrimeR")
virs <- basename(list.dirs(virus.folder, recursive = FALSE))
return(virs)
}
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