pyrox.dev
1diff --git a/R/AFND_interface.R b/R/AFND_interface.R
2index 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
18diff --git a/R/external_resources_input.R b/R/external_resources_input.R
19index 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")))