#' @title Prepare libraries of structure organism pairs LOTUS
#'
#' @description This function prepares the LOTUS structure-organism pairs
#'
#' @include fake_sop_columns.R
#' @include round_reals.R
#' @include select_sop_columns.R
#'
#' @param input Input file
#' @param output Output file
#'
#' @return NULL
#'
#' @export
#'
#' @examples NULL
prepare_libraries_sop_lotus <-
function(input = get_params(step = "prepare_libraries_sop_lotus")$files$libraries$sop$raw$lotus,
output = get_params(step = "prepare_libraries_sop_lotus")$files$libraries$sop$prepared$lotus) {
if (file.exists(input)) {
log_debug(x = "Loading and preparing LOTUS")
lotus_prepared <- input |>
tidytable::fread(
na.strings = c("", "NA"),
colClasses = "character"
) |>
tidytable::mutate(
structure_inchikey_2D = stringi::stri_sub(
str = structure_inchikey,
from = 1,
to = 14
)
) |>
tidytable::rename(structure_name = structure_nameTraditional) |>
select_sop_columns() |>
round_reals() |>
tidytable::distinct()
} else {
log_debug("Sorry, LOTUS not found, returning an empty file instead")
lotus_prepared <- fake_sop_columns()
}
log_debug(x = "Exporting ...")
export_output(x = lotus_prepared, file = output)
rm(lotus_prepared)
return(output)
}
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