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