R/cett_polypeptide_general_infromation_parsers.R

In Dainanahan/dbparser: Drugs Databases Parser

CETTPolyGeneralInfoParser <-
  R6::R6Class(
    "CETTPolyGeneralInfoParser",
    inherit = AbstractParser,
    private = list(
      parse_record = function() {
        cett_type <- strsplit(private$tibble_name, "_")[[1]][1]
        drugs <-  xmlChildren(pkg_env$root)
        pb <- progress_bar$new(total = xmlSize(drugs))
        polypeptides_tbl <-
          map_df(drugs,
                 ~ private$polypeptides_parser(., cett_type, pb)) %>% unique()
      },
      polypeptides_parser = function(rec, cett_type, pb) {
        pb$tick()
        parent_name <- paste0(substr(x     = cett_type,
                                     start = 1,
                                     stop  = nchar(cett_type)-1),
                              "_id")
        map_df(xmlChildren(rec[[cett_type]]),
               ~ private$polypeptide_rec(., parent_name))
      },
      polypeptide_rec = function(r, parent_name) {
        p_table   <- NULL
        parent_id <- xmlValue(r[["id"]])
        p         <- r[["polypeptide"]]

        if (!is.null(p)) {
          p_table <- tibble(
            polypeptide_id = ifelse(is.null(xmlGetAttr(p, name = "id")), NA,
                                    xmlGetAttr(p, name = "id")),
            source = ifelse(is.null(xmlGetAttr(p,
                                               name = "source")), NA,
                            xmlGetAttr(p, name = "source")),
            name = xmlValue(p[["name"]]),
            general_function = xmlValue(p[["general-function"]]),
            specific_function = xmlValue(p[["specific-function"]]),
            gene_name = xmlValue(p[["gene-name"]]),
            locus = xmlValue(p[["locus"]]),
            cellular_location = xmlValue(p[["cellular-location"]]),
            transmembrane_regions = xmlValue(p[["transmembrane-regions"]]),
            signal_regions = xmlValue(p[["signal-regions"]]),
            theoretical_pi = xmlValue(p[["theoretical-pi"]]),
            molecular_weight = xmlValue(p[["molecular-weight"]]),
            chromosome_location = xmlValue(p[["chromosome_location"]]),
            organism = xmlValue(p[["organism"]]),
            organism_ncbi_taxonomy_id = xmlGetAttr(p[["organism"]],
                                                   name = "ncbi-taxonomy-id"),
            amino_acid_sequence = xmlValue(p[["amino-acid-sequence"]]),
            amino_acid_format = xmlGetAttr(p[["amino-acid-sequence"]],
                                           name = "format"),
            gene_sequence = xmlValue(p[["gene-sequence"]]),
            gene_format = xmlGetAttr(p[["gene-sequence"]],
                                     name = "format")
          )

          p_table[[parent_name]] <- parent_id
        }

        p_table
      }
    )
  )

#' Carriers/ Enzymes/ Targets/ Transporters Polypeptide parsers
#'
#' Extract descriptions of identified polypeptide targets, enzymes, carriers,
#'  or transporters.
#'
#'
#' @return a tibble with 20 variables:
#' \describe{
#'   \item{id}{\href{https://www.uniprot.org/}{Universal Protein Resource
#'   (UniProt) identifier}}
#'   \item{source}{Specifies whether the identified polypeptide ID is
#'   associated with any of the following UniProt knowledge bases:
#'   Swiss-Prot, which is manually annotated and reviewed, or TrEMBL,
#'   which is automatically annotated and not reviewed.}
#'   \item{name}{}
#'   \item{general_function}{General summary of the physiological function of
#'   the polypeptide}
#'   \item{specific_function}{A more specific description of the polypeptide’s
#'    physiological function within the cell.}
#'   \item{gene_name}{The short name commonly associated with the associated
#'    gene. Eg. PTGS1.}
#'   \item{locus}{The specific chromosomal location or position of the gene’s
#'    sequence on a chromosome.}
#'   \item{cellular_location}{The cellular location of the polypeptide.}
#'   \item{transmembrane_regions}{Areas of the polypeptide sequence that span
#'    a biological membrane.}
#'   \item{signal_regions}{Location of any signal peptides within the
#'    polypeptide sequence.}
#'   \item{theoretical_pi}{Theoretical isoelectric point.}
#'   \item{molecular_weight}{The molecular weight of the polypeptide.}
#'   \item{chromosome_location}{The chromosomal location of the polypeptide
#'   gene}
#'   \item{organism}{The organism in which this polypeptide functions.}
#'   \item{organism_ncbi_taxonomy_id}{}
#'   \item{amino_acid_sequence}{The amino acid sequence of the polypeptide}
#'   \item{amino_acid_format}{}
#'   \item{gene_sequence}{The sequence of the associated gene.}
#'   \item{gene_format}{}
#'   \item{parent_key}{carrier/ target/ enzyme/ transporter id}
#' }
#' @keywords internal
#' @name cett_poly_doc
NULL

#' @rdname cett_poly_doc
carriers_polypeptides <- function() {
  CETTPolyGeneralInfoParser$new(
    "carriers_polypeptides"
  )$parse()
}

#' @rdname cett_poly_doc
enzymes_polypeptides <- function() {
  CETTPolyGeneralInfoParser$new(
    "enzymes_polypeptides"
  )$parse()
}

#' @rdname cett_poly_doc
targets_polypeptides <- function() {
  CETTPolyGeneralInfoParser$new(
    "targets_polypeptides"
  )$parse()
}

#' @rdname cett_poly_doc
transporters_polypeptides <- function() {
  CETTPolyGeneralInfoParser$new(
    "transporters_polypeptides"
  )$parse()
}