Mercurial > repos > iuc > pmids_to_pubtator_matrix

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

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
author iuc
date Wed, 24 Mar 2021 08:33:56 +0000
parents
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0
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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diff changeset
1 #!/usr/bin/env Rscript
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2 #TOOL2 abstracts_by_pmids
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3 #
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4 #This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
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5 #
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6 #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.
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7 #
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8 #Output: Input table with additional columns containing abstracts corresponding to the PMIDs from PubMed.
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9 #The abstract columns are called "ABSTRACT_1", "ABSTARCT_2" etc.
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10 #
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11 # Usage: $ T2_abstracts_by_pmid.R [-h] [-i INPUT] [-o OUTPUT]
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12 #
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13 # optional arguments:
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14 # -h, --help show help message
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15 # -i INPUT, --input INPUT input file name. add path if file is not in working directory
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16 # -o OUTPUT, --output OUTPUT output file name. [default "T2_output"]
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19 if ("--install_packages" %in% commandArgs()) {
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20 print("Installing packages")
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21 if (!require("argparse")) install.packages("argparse", repo = "http://cran.rstudio.com/");
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22 if (!require("reutils")) install.packages("reutils", repo = "http://cran.rstudio.com/");
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23 if (!require("easyPubMed")) install.packages("easyPubMed", repo = "http://cran.rstudio.com/");
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24 if (!require("textclean")) install.packages("textclean", repo = "http://cran.rstudio.com/");
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25 }
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26
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27 suppressPackageStartupMessages(library("argparse"))
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28 library("reutils")
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29 suppressPackageStartupMessages(library("easyPubMed"))
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30 suppressPackageStartupMessages(library("textclean"))
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32 parser <- ArgumentParser()
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33 parser$add_argument("-i", "--input",
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34 help = "input fie name. add path if file is not in workind directory")
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35 parser$add_argument("-o", "--output", default = "abstracts_by_pmids_output",
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36 help = "output file name. [default \"%(default)s\"]")
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37 parser$add_argument("--install_packages", action = "store_true", default = FALSE,
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38 help = "If you want to auto install missing required packages.")
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39
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40 args <- parser$parse_args()
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42 data <- read.delim(args$input, stringsAsFactors = FALSE, header = TRUE, sep = "\t")
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43 pmids_cols_index <- grep("PMID", names(data))
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44
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45 fetch_abstracts <- function(pmids, row) {
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46
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47 efetch_result <- NULL
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48 try_num <- 1
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49 t_0 <- Sys.time()
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50
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51 while (is.null(efetch_result)) {
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52
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53 # Timing check: kill at 3 min
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54 if (try_num > 1) {
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55 Sys.sleep(time = 1 * try_num)
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56 cat("Problem to receive PubMed data or error is received. Please wait. Try number: ", try_num, "\n")
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57 }
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58
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59 t_1 <- Sys.time()
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60
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61 if (as.numeric(difftime(t_1, t_0, units = "mins")) > 3) {
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62 message("Killing the request! Something is not working. Please, try again later", "\n")
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63 return(data)
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64 }
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65
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66 efetch_result <- tryCatch({
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67 suppressWarnings(efetch(uid = pmids, db = "pubmed", retmode = "xml"))
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68 }, error = function(e) {
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69 NULL
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70 })
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71
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72 if (!is.null(as.list(efetch_result$errors)$error)) {
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73 if (as.list(efetch_result$errors)$error == "HTTP error: Status 400; Bad Request") {
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74 efetch_result <- NULL
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75 }
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76 }
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77
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78 try_num <- try_num + 1
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79
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80 } #while loop end
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81
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82 # articles to list
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83 xml_data <- strsplit(efetch_result$content, "<PubmedArticle(>|[[:space:]]+?.*>)")[[1]][-1]
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84 xml_data <- sapply(xml_data, function(x) {
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85 #trim extra stuff at the end of the record
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86 if (!grepl("</PubmedArticle>$", x))
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87 x <- sub("(^.*</PubmedArticle>).*$", "\\1", x)
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88 # Rebuid XML structure and proceed
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89 x <- paste("<PubmedArticle>", x)
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90 gsub("[[:space:]]{2,}", " ", x)},
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91 USE.NAMES = FALSE, simplify = TRUE)
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92
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iuc
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93 abstract_text <- sapply(xml_data, function(x) {
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iuc
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94 custom_grep(x, tag = "AbstractText", format = "char")},
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iuc
parents:
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95 USE.NAMES = FALSE, simplify = TRUE)
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parents:
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96
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iuc
parents:
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97 abstracts <- sapply(abstract_text, function(x) {
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iuc
parents:
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98 if (length(x) > 1) {
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iuc
parents:
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99 x <- paste(x, collapse = " ", sep = " ")
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iuc
parents:
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100 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
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iuc
parents:
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101 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
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iuc
parents:
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102 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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103 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
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iuc
parents:
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104 } else if (length(x) < 1) {
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iuc
parents:
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105 x <- NA
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iuc
parents:
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106 } else {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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107 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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108 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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109 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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110 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
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iuc
parents:
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111 }
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iuc
parents:
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112 x
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iuc
parents:
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113 },
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iuc
parents:
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114 USE.NAMES = FALSE, simplify = TRUE)
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parents:
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115
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iuc
parents:
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116 abstracts <- as.character(abstracts)
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117
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iuc
parents:
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118 if (length(abstracts) > 0) {
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iuc
parents:
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119 data[row, sapply(seq(length(abstracts)), function(i) {
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iuc
parents:
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120 paste0("ABSTRACT_", i)
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iuc
parents:
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121 })] <- abstracts
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iuc
parents:
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122 cat(length(abstracts), " abstracts for PMIDs of row ", row, " are added in the table.", "\n")
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iuc
parents:
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123 }
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124
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iuc
parents:
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125 return(data)
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iuc
parents:
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126 }
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127
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parents:
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128
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iuc
parents:
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129 for (row in seq(nrow(data))) {
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iuc
parents:
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130 pmids <- as.character(unique(data[row, pmids_cols_index]))
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iuc
parents:
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131 pmids <- pmids[!pmids == "NA"]
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132
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iuc
parents:
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133 if (length(pmids) > 0) {
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iuc
parents:
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134 data <- tryCatch(fetch_abstracts(pmids, row),
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iuc
parents:
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135 error = function(e) {
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iuc
parents:
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136 Sys.sleep(3)
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iuc
parents:
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137 })
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iuc
parents:
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138 } else {
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iuc
parents:
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139 print(paste("No PMIDs in row", row))
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iuc
parents:
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140 }
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iuc
parents:
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141 }
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iuc
parents:
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142 write.table(data, args$output, sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)