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

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

#!/usr/bin/env Rscript
#tool: pmids_to_pubtator_matrix
#
#The tool uses all PMIDs per row and extracts "Gene", "Disease", "Mutation", "Chemical" and "Species" terms of the
#corresponding abstracts, using PubTator annotations. The user can choose from which categories terms should be extracted.
#The extracted terms are united in one large binary matrix, with 0= term not present in abstracts of that row and 1= term
#present in abstracts of that row. The user can decide if the extracted scientific terms should be extracted and used as
#they are or if they should be grouped by their geneIDs/ meshIDs (several terms can often be grouped into one ID).
#äAlso, by default all terms are extracted, otherwise the user can specify a number of most frequent words to be extracted per row.
#
#Input: Output of abstracts_by_pmids or 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: Binary matrix in that each column represents one of the extracted terms.
#
# usage: $ pmids_to_pubtator_matrix.R [-h] [-i INPUT] [-o OUTPUT] [-n NUMBER]
# [-c {Genes,Diseases,Mutations,Chemicals,Species} [{Genes,Diseases,Mutations,Chemicals,Species} ...]]
#
# optional arguments:
#   -h, --help                 show help message
#   -i INPUT, --input INPUT    input file name. add path if file is not in workind directory
#   -n NUMBER, --number NUMBER Number of most frequent terms/IDs to extract. By default all terms/IDs are extracted.
#   -o OUTPUT, --output OUTPUT output file name. [default "pmids_to_pubtator_matrix_output"]
#   -c {Gene,Disease,Mutation,Chemical,Species} [{Genes,Diseases,Mutations,Chemicals,Species} ...], --categories {Gene,Disease,Mutation,Chemical,Species} [{Gene,Disease,Mutation,Chemical,Species} ...]
#      Pubtator categories that should be considered.  [default "('Gene', 'Disease', 'Mutation','Chemical')"]

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

suppressPackageStartupMessages(library("argparse"))
library("stringr")
library("RCurl")
library("stringi")

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 = "pmids_to_pubtator_matrix_output",
                    help = "output file name. [default \"%(default)s\"]")
parser$add_argument("-c", "--categories", choices = c("Gene", "Disease", "Mutation", "Chemical", "Species"), nargs = "+",
                    default = c("Gene", "Disease", "Mutation", "Chemical"),
                    help = "Pubtator categories that should be considered. [default \"%(default)s\"]")
parser$add_argument("-b", "--byid", action = "store_true", default = FALSE,
                    help = "If you want to find common gene IDs / mesh IDs instead of scientific terms.")
parser$add_argument("-n", "--number", default = NULL, type = "integer",
                    help = "Number of most frequent terms/IDs to extract. By default all terms/IDs are extracted.")
parser$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")

pmid_cols_index <- grep(c("PMID"), names(data))
word_matrix <- data.frame()
dict_table <- data.frame()
pmids_count <- 0
pubtator_max_ids <- 100


merge_pubtator_table <- function(out_data, table) {
  out_data <- unlist(strsplit(out_data, "\n", fixed = T))
  for (i in 3:length(out_data)) {
    temps <- unlist(strsplit(out_data[i], "\t", fixed = T))
    if (length(temps) == 5) {
      temps <- c(temps, NA)
    }
    if (length(temps) == 6) {
      table <- rbind(table, temps)
    }
  }
  return(table)
}


get_pubtator_terms <- function(pmids) {
  table <- NULL
  for (pmid_split in split(pmids, ceiling(seq_along(pmids) / pubtator_max_ids))) {
    out_data <- NULL
    try_num <- 1
    t_0 <- Sys.time()
    while (TRUE) {
      # Timing check: kill at 3 min
      if (try_num > 1) {
        cat("Connection problem. Please wait. Try number:", try_num, "\n")
        Sys.sleep(time = 2 * try_num)
      }
      try_num <- try_num + 1
      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(table)
      }
      out_data <- tryCatch({
        getURL(paste("https://www.ncbi.nlm.nih.gov/research/pubtator-api/publications/export/pubtator?pmids=",
                     paste(pmid_split, collapse = ","), sep = ""))
      }, error = function(e) {
        print(e)
        next
      }, finally = {
        Sys.sleep(0)
      })
      if (!is.null(out_data)) {
        table <- merge_pubtator_table(out_data, table)
        break
      }
    }
  }
  return(table)
}

extract_category_terms <- function(table, categories) {
  index_categories <- c()
  categories <- as.character(unlist(categories))
  if (ncol(table) == 6) {
    for (i in categories) {
      tmp_index <- grep(TRUE, i == as.character(table[, 5]))
      if (length(tmp_index) > 0) {
        index_categories <- c(index_categories, tmp_index)
      }
    }
    table <- as.data.frame(table, stringsAsFactors = FALSE)
    table <- table[index_categories, c(4, 6)]
    table <- table[!is.na(table[, 2]), ]
    table <- table[!(table[, 2] == "NA"), ]
    table <- table[!(table[, 1] == "NA"), ]
  }else{
    return(NULL)
  }
}

extract_frequent_ids_or_terms <- function(table) {
  if (is.null(table)) {
    return(NULL)
    break
  }
  if (args$byid) {
    if (!is.null(args$number)) {
      #retrieve top X mesh_ids
      table_mesh <- as.data.frame(table(table[, 2]))
      colnames(table_mesh)[1] <- "mesh_id"
      table <- table[order(table_mesh$Freq, decreasing = TRUE), ]
      table <- table[1:min(args$number, nrow(table_mesh)), ]
      table_mesh$mesh_id <- as.character(table_mesh$mesh_id)
      #subset table for top X mesh_ids
      table <- table[which(as.character(table$V6) %in% as.character(table_mesh$mesh_id)), ]
      table <- table[!duplicated(table[, 2]), ]
    } else {
      table <- table[!duplicated(table[, 2]), ]
    }
  } else {
    if (!is.null(args$number)) {
      table[, 1] <- tolower(as.character(table[, 1]))
      table <- as.data.frame(table(table[, 1]))
      colnames(table)[1] <- "term"
      table <- table[order(table$Freq, decreasing = TRUE), ]
      table <- table[1:min(args$number, nrow(table)), ]
      table$term <- as.character(table$term)
    } else {
      table[, 1] <- tolower(as.character(table[, 1]))
      table <- table[!duplicated(table[, 1]), ]
    }
  }
  return(table)
}


#for all PMIDs of a row get PubTator terms and add them to the matrix
for (i in seq(nrow(data))) {
  pmids <- as.character(data[i, pmid_cols_index])
  pmids <- pmids[!pmids == "NA"]
  if (pmids_count > 10000) {
    cat("Break (10s) to avoid killing of requests. Please wait.", "\n")
    Sys.sleep(10)
    pmids_count <- 0
  }
  pmids_count <- pmids_count + length(pmids)
  #get puptator terms and process them with functions
  if (length(pmids) > 0) {
    table <- get_pubtator_terms(pmids)
    table <- extract_category_terms(table, args$categories)
    table <- extract_frequent_ids_or_terms(table)
    if (!is.null(table)) {
      colnames(table) <- c("term", "mesh_id")
      # add data in binary matrix
      if (args$byid) {
        mesh_ids <- as.character(table$mesh_id)
        if (length(mesh_ids) > 0) {
          word_matrix[i, mesh_ids] <- 1
          cat(length(mesh_ids), " IDs for PMIDs of row", i, " were added", "\n")
          # add data in dictionary
          dict_table <- rbind(dict_table, table)
          dict_table <- dict_table[!duplicated(as.character(dict_table[, 2])), ]
        }
      } else {
        terms <- as.character(table[, 1])
        if (length(terms) > 0) {
          word_matrix[i, terms] <- 1
          cat(length(terms), " terms for PMIDs of row", i, " were added.", "\n")
        }
      }
    }
  } else {
    cat("No terms for PMIDs of row", i, " were found.", "\n")
  }
}

if (args$byid) {
  #change column names of matrix: exchange mesh ids/ids with term
  index_names <- match(names(word_matrix), as.character(dict_table[[2]]))
  names(word_matrix) <- dict_table[index_names, 1]
}

colnames(word_matrix) <- gsub("[^[:print:]]", "", colnames(word_matrix))
colnames(word_matrix) <- gsub('\"', "", colnames(word_matrix), fixed = TRUE)

#merge duplicated columns
word_matrix <- as.data.frame(do.call(cbind, by(t(word_matrix), INDICES = names(word_matrix), FUN = colSums)))

#save binary matrix
word_matrix <- as.matrix(word_matrix)
word_matrix[is.na(word_matrix)] <- 0
cat("Matrix with ", nrow(word_matrix), " rows and ", ncol(word_matrix), " columns generated.", "\n")
write.table(word_matrix, args$output, row.names = FALSE, sep = "\t", quote = FALSE)