pkgs/development/r-modules/patches/immunotation.patch

   1 diff --git a/R/AFND_interface.R b/R/AFND_interface.R
   2 index b62e8e0..0f22d85 100644
   3 --- a/R/AFND_interface.R
   4 +++ b/R/AFND_interface.R
   5 @@ -244,9 +244,9 @@ check_population <- function(hla_population) {
   6  #' @return list of valid countries, regions and ethnic origin
   7  #' @keywords internal
   8  get_valid_geographics <- function() {
   9 -    url <- "http://www.allelefrequencies.net/hla6006a.asp?"
  10 -    html_input <- getURL(url, read_method = "html")
  11 -
  12 +    # http://www.allelefrequencies.net/hla6006a.asp?
  13 +    html_input <- xml2::read_html("nix-valid-geographics")
  14 +
  15      rvest_tables <- rvest::html_table(html_input, fill = TRUE)
  16
  17      # country
  18 diff --git a/R/external_resources_input.R b/R/external_resources_input.R
  19 index c4b1dc1..8fc5881 100644
  20 --- a/R/external_resources_input.R
  21 +++ b/R/external_resources_input.R
  22 @@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L,
  23  # MHC I
  24  # netmhcI_input_template is an internal variable containing list of valid
  25  # NetMHCpan input alleles
  26 -netmhcI_input_template <- getURL(
  27 -    URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list",
  28 -    read_method = "delim", delim = "\t",
  29 -    col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))
  30 +netmhcI_input_template <- readr::read_delim(
  31 +        # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list
  32 +       "nix-NetMHCpan-4.1-allele-list",
  33 +       delim = "\t",
  34 +       skip = 0,
  35 +        col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")
  36 +    )
  37
  38  # MHC II
  39 -lines <- getURL(
  40 -    URL = paste0("https://services.healthtech.dtu.dk/services/",
  41 -    "NetMHCIIpan-4.0/alleles_name.list"),
  42 -    read_method = "lines")
  43 +# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list
  44 +lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list")
  45  lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t")
  46  netmhcII_input_template <- suppressWarnings(
  47      suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))