annotate abstracts_by_pmids.R @ 0:69714f06f18b draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"

#!/usr/bin/env Rscript
#TOOL2 abstracts_by_pmids
#
#This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
#
#Input: Tab-delimited table with columns containing PMIDs. The names of the PMID columns should start with “PMID”, e.g. “PMID_1”, “PMID_2” etc.
#
#Output: Input table with additional columns containing abstracts corresponding to the PMIDs from PubMed.
#The abstract columns are called "ABSTRACT_1", "ABSTARCT_2" etc.
#
# Usage: $ T2_abstracts_by_pmid.R [-h] [-i INPUT] [-o OUTPUT]
#
# optional arguments:
# -h, --help                 show help message
# -i INPUT, --input INPUT    input file name. add path if file is not in working directory
# -o OUTPUT, --output OUTPUT output file name. [default "T2_output"]


if ("--install_packages" %in% commandArgs()) {
  print("Installing packages")
  if (!require("argparse")) install.packages("argparse", repo = "http://cran.rstudio.com/");
  if (!require("reutils")) install.packages("reutils", repo = "http://cran.rstudio.com/");
  if (!require("easyPubMed")) install.packages("easyPubMed", repo = "http://cran.rstudio.com/");
  if (!require("textclean")) install.packages("textclean", repo = "http://cran.rstudio.com/");
}

suppressPackageStartupMessages(library("argparse"))
library("reutils")
suppressPackageStartupMessages(library("easyPubMed"))
suppressPackageStartupMessages(library("textclean"))

parser <- ArgumentParser()
parser$add_argument("-i", "--input",
                    help = "input fie name. add path if file is not in workind directory")
parser$add_argument("-o", "--output", default = "abstracts_by_pmids_output",
                    help = "output file name. [default \"%(default)s\"]")
parser$add_argument("--install_packages", action = "store_true", default = FALSE,
                    help = "If you want to auto install missing required packages.")

args <- parser$parse_args()

data <- read.delim(args$input, stringsAsFactors = FALSE, header = TRUE, sep = "\t")
pmids_cols_index <- grep("PMID", names(data))

fetch_abstracts <- function(pmids, row) {

  efetch_result <- NULL
  try_num <- 1
  t_0 <- Sys.time()

  while (is.null(efetch_result)) {

    # Timing check: kill at 3 min
    if (try_num > 1) {
      Sys.sleep(time = 1 * try_num)
      cat("Problem to receive PubMed data or error is received. Please wait. Try number: ", try_num, "\n")
    }

    t_1 <- Sys.time()

    if (as.numeric(difftime(t_1, t_0, units = "mins")) > 3) {
      message("Killing the request! Something is not working. Please, try again later", "\n")
      return(data)
    }

    efetch_result <- tryCatch({
      suppressWarnings(efetch(uid = pmids, db = "pubmed", retmode = "xml"))
    }, error = function(e) {
      NULL
    })

    if (!is.null(as.list(efetch_result$errors)$error)) {
      if (as.list(efetch_result$errors)$error == "HTTP error: Status 400; Bad Request") {
        efetch_result <- NULL
      }
    }

    try_num <- try_num + 1

  } #while loop end

  # articles to list
  xml_data <- strsplit(efetch_result$content, "<PubmedArticle(>|[[:space:]]+?.*>)")[[1]][-1]
  xml_data <- sapply(xml_data, function(x) {
    #trim extra stuff at the end of the record
    if (!grepl("</PubmedArticle>$", x))
      x <- sub("(^.*</PubmedArticle>).*$", "\\1", x)
    # Rebuid XML structure and proceed
    x <- paste("<PubmedArticle>", x)
    gsub("[[:space:]]{2,}", " ", x)},
    USE.NAMES = FALSE, simplify = TRUE)

  abstract_text <- sapply(xml_data, function(x) {
    custom_grep(x, tag = "AbstractText", format = "char")},
    USE.NAMES = FALSE, simplify = TRUE)

  abstracts <- sapply(abstract_text, function(x) {
    if (length(x) > 1) {
      x <- paste(x, collapse = " ", sep = " ")
      x <- gsub("</{0,1}i>", "", x, ignore.case = T)
      x <- gsub("</{0,1}b>", "", x, ignore.case = T)
      x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
      x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
    } else if (length(x) < 1) {
      x <- NA
    } else {
      x <- gsub("</{0,1}i>", "", x, ignore.case = T)
      x <- gsub("</{0,1}b>", "", x, ignore.case = T)
      x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
      x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
    }
    x
  },
  USE.NAMES = FALSE, simplify = TRUE)

  abstracts <- as.character(abstracts)

  if (length(abstracts) > 0) {
    data[row, sapply(seq(length(abstracts)), function(i) {
      paste0("ABSTRACT_", i)
      })] <- abstracts
    cat(length(abstracts), " abstracts for PMIDs of row ", row, " are added in the table.", "\n")
  }

  return(data)
}
    

for (row in seq(nrow(data))) {
  pmids <-  as.character(unique(data[row, pmids_cols_index]))
  pmids <- pmids[!pmids == "NA"]

  if (length(pmids) > 0) {
    data <- tryCatch(fetch_abstracts(pmids, row),
                    error = function(e) {
                      Sys.sleep(3)
                      })
  } else {
    print(paste("No PMIDs in row", row))
  }
}
write.table(data, args$output, sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)