R/prepare_libraries_sop_ecmdb.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Prepare libraries of structure organism pairs ECMDB
#'
#' @include fake_sop_columns.R
#' @include get_params.R
#' @include round_reals.R
#' @include select_sop_columns.R
#'
#' @param input Input file
#' @param output Output file
#'
#' @return The path to the prepared structure-organism pairs library ECMDB
#'
#' @export
#'
#' @examples
#' \dontrun{
#' copy_backbone()
#' go_to_cache()
#' prepare_libraries_sop_ecmdb()
#' unlink("data", recursive = TRUE)
#' }
prepare_libraries_sop_ecmdb <-
  function(
    input = get_params(
      step = "prepare_libraries_sop_ecmdb"
    )$files$libraries$sop$raw$ecmdb,
    output = get_params(
      step = "prepare_libraries_sop_ecmdb"
    )$files$libraries$sop$prepared$ecmdb
  ) {
    if (!file.exists(output) || file.size(output) < 100000) {
      if (file.exists(input)) {
        logger::log_trace("Loading ECMDB resources")

        file <- gsub(
          pattern = ".zip",
          replacement = "",
          x = input,
          fixed = TRUE
        ) |>
          gsub(
            pattern = ".*/",
            replacement = "",
            perl = TRUE
          )

        ecmdb <- jsonlite::stream_in(
          con = unz(description = input, filename = file),
          verbose = FALSE
        ) |>
          data.frame() |>
          tidytable::as_tidytable()

        logger::log_trace("Formatting ECMDB")
        ecmdb_prepared <- ecmdb |>
          tidytable::mutate(
            structure_inchikey_2D = stringi::stri_sub(
              str = moldb_inchikey,
              from = 1,
              to = 14
            ),
            structure_smiles_2D = NA_character_
          ) |>
          tidytable::rename(
            structure_name = name,
            structure_inchikey = moldb_inchikey,
            structure_smiles = moldb_smiles,
            structure_molecular_formula = moldb_formula,
            structure_exact_mass = moldb_mono_mass,
            structure_xlogp = moldb_logp
          ) |>
          tidytable::mutate(
            structure_taxonomy_npclassifier_01pathway = NA_character_,
            structure_taxonomy_npclassifier_02superclass = NA_character_,
            structure_taxonomy_npclassifier_03class = NA_character_,
            structure_taxonomy_classyfire_chemontid = NA_character_,
            structure_taxonomy_classyfire_01kingdom = NA_character_,
            structure_taxonomy_classyfire_02superclass = NA_character_,
            structure_taxonomy_classyfire_03class = NA_character_,
            structure_taxonomy_classyfire_04directparent = NA_character_
          ) |>
          tidytable::mutate(
            organism_name = "Escherichia coli",
            organism_taxonomy_ottid = 474506,
            organism_taxonomy_01domain = "Bacteria",
            organism_taxonomy_02kingdom = NA_character_,
            organism_taxonomy_03phylum = "Proteobacteria",
            organism_taxonomy_04class = "Gammaproteobacteria",
            organism_taxonomy_05order = "Enterobacteriales",
            organism_taxonomy_06family = "Enterobacteriaceae",
            organism_taxonomy_07tribe = NA_character_,
            organism_taxonomy_08genus = NA_character_,
            organism_taxonomy_09species = "Escherichia coli",
            organism_taxonomy_10varietas = NA_character_
          ) |>
          tidytable::mutate(reference_doi = NA) |>
          select_sop_columns() |>
          round_reals() |>
          tidytable::distinct()
        rm(ecmdb)
      } else {
        logger::log_warn(
          "Sorry, ECMDB not found, returning an empty file instead"
        )
        ecmdb_prepared <- fake_sop_columns()
      }

      export_params(
        parameters = get_params(step = "prepare_libraries_sop_ecmdb"),
        step = "prepare_libraries_sop_ecmdb"
      )
      export_output(x = ecmdb_prepared, file = output)
      rm(ecmdb_prepared)
    }
    return(output)
  }