1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
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")))
|
