diff options
Diffstat (limited to 'pkgs/development/r-modules/patches/immunotation.patch')
-rw-r--r-- | pkgs/development/r-modules/patches/immunotation.patch | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/pkgs/development/r-modules/patches/immunotation.patch b/pkgs/development/r-modules/patches/immunotation.patch new file mode 100644 index 000000000000..2019e8e50a02 --- /dev/null +++ b/pkgs/development/r-modules/patches/immunotation.patch @@ -0,0 +1,47 @@ +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"))) |