Mercurial > repos > iuc > pmids_to_pubtator_matrix

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
children
comparison
equal deleted inserted replaced
-1:000000000000 0:69714f06f18b
1 #!/usr/bin/env Rscript
2 #TOOL2 abstracts_by_pmids
3 #
4 #This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
5 #
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.
7 #
8 #Output: Input table with additional columns containing abstracts corresponding to the PMIDs from PubMed.
9 #The abstract columns are called "ABSTRACT_1", "ABSTARCT_2" etc.
10 #
11 # Usage: $ T2_abstracts_by_pmid.R [-h] [-i INPUT] [-o OUTPUT]
12 #
13 # optional arguments:
14 # -h, --help show help message
15 # -i INPUT, --input INPUT input file name. add path if file is not in working directory
16 # -o OUTPUT, --output OUTPUT output file name. [default "T2_output"]
17
18
19 if ("--install_packages" %in% commandArgs()) {
20 print("Installing packages")
21 if (!require("argparse")) install.packages("argparse", repo = "http://cran.rstudio.com/");
22 if (!require("reutils")) install.packages("reutils", repo = "http://cran.rstudio.com/");
23 if (!require("easyPubMed")) install.packages("easyPubMed", repo = "http://cran.rstudio.com/");
24 if (!require("textclean")) install.packages("textclean", repo = "http://cran.rstudio.com/");
25 }
26
27 suppressPackageStartupMessages(library("argparse"))
28 library("reutils")
29 suppressPackageStartupMessages(library("easyPubMed"))
30 suppressPackageStartupMessages(library("textclean"))
31
32 parser <- ArgumentParser()
33 parser$add_argument("-i", "--input",
34 help = "input fie name. add path if file is not in workind directory")
35 parser$add_argument("-o", "--output", default = "abstracts_by_pmids_output",
36 help = "output file name. [default \"%(default)s\"]")
37 parser$add_argument("--install_packages", action = "store_true", default = FALSE,
38 help = "If you want to auto install missing required packages.")
39
40 args <- parser$parse_args()
41
42 data <- read.delim(args$input, stringsAsFactors = FALSE, header = TRUE, sep = "\t")
43 pmids_cols_index <- grep("PMID", names(data))
44
45 fetch_abstracts <- function(pmids, row) {
46
47 efetch_result <- NULL
48 try_num <- 1
49 t_0 <- Sys.time()
50
51 while (is.null(efetch_result)) {
52
53 # Timing check: kill at 3 min
54 if (try_num > 1) {
55 Sys.sleep(time = 1 * try_num)
56 cat("Problem to receive PubMed data or error is received. Please wait. Try number: ", try_num, "\n")
57 }
58
59 t_1 <- Sys.time()
60
61 if (as.numeric(difftime(t_1, t_0, units = "mins")) > 3) {
62 message("Killing the request! Something is not working. Please, try again later", "\n")
63 return(data)
64 }
65
66 efetch_result <- tryCatch({
67 suppressWarnings(efetch(uid = pmids, db = "pubmed", retmode = "xml"))
68 }, error = function(e) {
69 NULL
70 })
71
72 if (!is.null(as.list(efetch_result$errors)$error)) {
73 if (as.list(efetch_result$errors)$error == "HTTP error: Status 400; Bad Request") {
74 efetch_result <- NULL
75 }
76 }
77
78 try_num <- try_num + 1
79
80 } #while loop end
81
82 # articles to list
83 xml_data <- strsplit(efetch_result$content, "<PubmedArticle(>|[[:space:]]+?.*>)")[[1]][-1]
84 xml_data <- sapply(xml_data, function(x) {
85 #trim extra stuff at the end of the record
86 if (!grepl("</PubmedArticle>$", x))
87 x <- sub("(^.*</PubmedArticle>).*$", "\\1", x)
88 # Rebuid XML structure and proceed
89 x <- paste("<PubmedArticle>", x)
90 gsub("[[:space:]]{2,}", " ", x)},
91 USE.NAMES = FALSE, simplify = TRUE)
92
93 abstract_text <- sapply(xml_data, function(x) {
94 custom_grep(x, tag = "AbstractText", format = "char")},
95 USE.NAMES = FALSE, simplify = TRUE)
96
97 abstracts <- sapply(abstract_text, function(x) {
98 if (length(x) > 1) {
99 x <- paste(x, collapse = " ", sep = " ")
100 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
101 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
102 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
103 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
104 } else if (length(x) < 1) {
105 x <- NA
106 } else {
107 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
108 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
109 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
110 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
111 }
112 x
113 },
114 USE.NAMES = FALSE, simplify = TRUE)
115
116 abstracts <- as.character(abstracts)
117
118 if (length(abstracts) > 0) {
119 data[row, sapply(seq(length(abstracts)), function(i) {
120 paste0("ABSTRACT_", i)
121 })] <- abstracts
122 cat(length(abstracts), " abstracts for PMIDs of row ", row, " are added in the table.", "\n")
123 }
124
125 return(data)
126 }
127
128
129 for (row in seq(nrow(data))) {
130 pmids <- as.character(unique(data[row, pmids_cols_index]))
131 pmids <- pmids[!pmids == "NA"]
132
133 if (length(pmids) > 0) {
134 data <- tryCatch(fetch_abstracts(pmids, row),
135 error = function(e) {
136 Sys.sleep(3)
137 })
138 } else {
139 print(paste("No PMIDs in row", row))
140 }
141 }
142 write.table(data, args$output, sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)