diff --git a/R/AFND_interface.R b/R/AFND_interface.R index b62e8e0..0f22d85 100644 --- a/R/AFND_interface.R +++ b/R/AFND_interface.R @@ -244,9 +244,9 @@ check_population <- function(hla_population) { #' @return list of valid countries, regions and ethnic origin #' @keywords internal get_valid_geographics <- function() { - url <- "http://www.allelefrequencies.net/hla6006a.asp?" - html_input <- getURL(url, read_method = "html") - + # http://www.allelefrequencies.net/hla6006a.asp? + html_input <- xml2::read_html("nix-valid-geographics") + rvest_tables <- rvest::html_table(html_input, fill = TRUE) # country diff --git a/R/external_resources_input.R b/R/external_resources_input.R index c4b1dc1..8fc5881 100644 --- a/R/external_resources_input.R +++ b/R/external_resources_input.R @@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L, # MHC I # netmhcI_input_template is an internal variable containing list of valid # NetMHCpan input alleles -netmhcI_input_template <- getURL( - URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list", - read_method = "delim", delim = "\t", - col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")) +netmhcI_input_template <- readr::read_delim( + # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list + "nix-NetMHCpan-4.1-allele-list", + delim = "\t", + skip = 0, + col_names = c("netmhc_input", "hla_chain_name", "HLA_gene") + ) # MHC II -lines <- getURL( - URL = paste0("https://services.healthtech.dtu.dk/services/", - "NetMHCIIpan-4.0/alleles_name.list"), - read_method = "lines") +# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list +lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list") lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t") netmhcII_input_template <- suppressWarnings( suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))