R/utils.R

In JBrowseR: An R Interface to the JBrowse 2 Genome Browser

get_name <- function(string) {
  if (is_url(string)) {
    # get assembly name from URL
    name <- parse_url_name(string)
  } else {
    # get assembly name from file
    name <- parse_file_name(string)
  }
}

is_url <- function(string) {
  grepl("www.|http:|https:", string)
}

parse_url_name <- function(url) {
  stringr::str_split(url, "/", simplify = TRUE) %>%
    last_value() %>%
    stringr::str_split("[.]", simplify = TRUE) %>%
    first_value()
}

parse_file_name <- function(path) {
  stringr::str_split(basename(path), "[.]", simplify = TRUE) %>%
    first_value()
}

last_value <- function(x) {
  x[length(x)]
}

first_value <- function(x) {
  x[1]
}

# get the name out of the assembly config string
get_assembly_name <- function(assembly) {
  assembly_list <- jsonlite::fromJSON(assembly)

  assembly_list$name
}

# get the assembly adapter out of the assembly config string
get_assembly_adapter <- function(assembly) {
  assembly_list <- jsonlite::fromJSON(assembly)
  adapter <- assembly_list$sequence$adapter

  jsonlite::toJSON(adapter, auto_unbox = TRUE)
}

strip_gz <- function(track_data) {
  if (stringr::str_ends(track_data, ".gz")) {
    stringr::str_trunc(track_data, nchar(track_data) - 3, "right", "")
  } else {
    track_data
  }
}