R/prepare_annotations_gnps.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Prepare annotations GNPS
#'
#' @description This function prepares GNPS obtained annotations
#'
#' @include get_params.R
#' @include select_annotations_columns.R
#'
#' @param input Input file
#' @param output Output file
#' @param str_stereo File containing structures stereo
#' @param str_met File containing structures metadata
#' @param str_nam File containing structures names
#' @param str_tax_cla File containing Classyfire taxonomy
#' @param str_tax_npc File containing NPClassifier taxonomy
#'
#' @return The path to the prepared GNPS annotations
#'
#' @export
#'
#' @examples
#' \dontrun{
#' tima:::copy_backbone()
#' go_to_cache()
#' prepare_annotations_gnps()
#' unlink("data", recursive = TRUE)
#' }
prepare_annotations_gnps <-
  function(input = get_params(step = "prepare_annotations_gnps")$files$annotations$raw$spectral$gnps,
           output = get_params(step = "prepare_annotations_gnps")$files$annotations$prepared$structural$gnps,
           str_stereo = get_params(step = "prepare_annotations_gnps")$files$libraries$sop$merged$structures$stereo,
           str_met = get_params(step = "prepare_annotations_gnps")$files$libraries$sop$merged$structures$metadata,
           str_nam = get_params(step = "prepare_annotations_gnps")$files$libraries$sop$merged$structures$names,
           str_tax_cla = get_params(step = "prepare_annotations_gnps")$files$libraries$sop$merged$structures$taxonomies$cla,
           str_tax_npc = get_params(step = "prepare_annotations_gnps")$files$libraries$sop$merged$structures$taxonomies$npc) {
    if (length(input) == 0) {
      input <- "w1llN3v3r3v3r3x1st"
    }
    if (all(purrr::map(.x = input, .f = file.exists) |> unlist())) {
      log_debug("Loading and formatting GNPS results")
      ## See https://github.com/CCMS-UCSD/GNPS_Workflows/issues/747
      table <- purrr::map(
        .x = input,
        .f = tidytable::fread,
        na.strings = c("", "NA"),
        colClasses = "character"
      ) |>
        tidytable::bind_rows() |>
        tidytable::mutate(candidate_structure_error_mz = as.numeric(MZErrorPPM) *
          1E-6 *
          as.numeric(Precursor_MZ)) |>
        tidytable::select(tidyselect::any_of(
          c(
            "feature_id" = "#Scan#",
            "candidate_adduct" = "Adduct",
            "candidate_structure_error_mz" = "MassDiff",
            "candidate_library" = "LibraryName",
            "candidate_structure_name" = "Compound_Name",
            "candidate_score_similarity" = "MQScore",
            "candidate_count_similarity_peaks_matched" = "SharedPeaks",
            "candidate_structure_inchi" = "INCHI",
            "candidate_structure_inchikey" = "InChIKey",
            "candidate_structure_inchikey_no_stereo" = "InChIKey-Planar",
            "candidate_structure_tax_npc_01pat" = "npclassifier_pathway",
            "candidate_structure_tax_npc_02sup" = "npclassifier_superclass",
            "candidate_structure_tax_npc_03cla" = "npclassifier_class",
            "candidate_structure_exact_mass" = "ExactMass",
            ## Only partially present
            "candidate_structure_tax_cla_02sup" = "superclass",
            "candidate_structure_tax_cla_03cla" = "class",
            "candidate_structure_tax_cla_04dirpar" = "subclass"
          )
        )) |>
        tidytable::mutate(
          candidate_structure_smiles_no_stereo = NA,
          candidate_structure_molecular_formula = candidate_structure_inchi |>
            ## really dirty
            gsub(
              pattern = ".*\\/C",
              replacement = "C",
              perl = TRUE
            ) |>
            gsub(
              pattern = "\\/.*",
              replacement = "",
              perl = TRUE
            ),
          candidate_structure_xlogp = NA,
          ## Only partially present
          candidate_structure_tax_cla_chemontid = NA,
          candidate_structure_tax_cla_01kin = NA
        ) |>
        tima:::select_annotations_columns()
    } else {
      log_debug("No GNPS annotations found, returning an empty file instead")
      table <- tima:::fake_annotations_columns()
    }

    tima:::export_params(
      parameters = get_params(step = "prepare_annotations_gnps"),
      step = "prepare_annotations_gnps"
    )
    tima:::export_output(x = table, file = output[[1]])
    rm(table)
    return(output[[1]])
  }