Mercurial > repos > dlalgroup > pmids_to_pubtator_matrix

annotate pubmed_by_queries.R @ 2:ada4c7b3fc39 draft default tip

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"planemo upload for repository https://github.com/dlal-group/simtext commit 63f67ee02be2eb4323a5ba5dcdd33d1fd0b7c24e"
author dlalgroup
date Thu, 08 Oct 2020 05:39:58 +0000
parents 3f4adc85ba5d
children
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1 #!/usr/bin/env Rscript
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2 #tool: pubmed_by_queries
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3 #
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4 #This tool uses a set of search queries to download a defined number of abstracts or PMIDs for search query from PubMed.
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5 #PubMed's search rules and syntax apply.
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6 #
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7 #Input: Tab-delimited table with search queries in a column starting with "ID_", e.g. "ID_gene" if search queries are genes.
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8 #
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9 # Output: Input table with additional columns with PMIDs or abstracts (--abstracts) from PubMed.
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10 #
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11 #Usage: $ pubmed_by_queries.R [-h] [-i INPUT] [-o OUTPUT] [-n NUMBER] [-a] [-k KEY]
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12 #
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13 # optional arguments:
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14 # -h, --help show this help message and exit
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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 "pubmed_by_queries_output"]
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17 # -n NUMBER, --number NUMBER number of PMIDs or abstracts to save per ID [default "5"]
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18 # -a, --abstract if abstracts instead of PMIDs should be retrieved use --abstracts
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19 # -k KEY, --key KEY if NCBI API key is available, add it to speed up the fetching of pubmed data
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20
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21 if ( '--install_packages' %in% commandArgs()) {
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22 print('Installing packages')
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23 if (!require('argparse')) install.packages('argparse',repo="http://cran.rstudio.com/");
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24 if (!require('easyPubMed')) install.packages('easyPubMed',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 suppressPackageStartupMessages(library("easyPubMed"))
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29
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30 parser <- ArgumentParser()
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31 parser$add_argument("-i", "--input",
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32 help = "input fie name. add path if file is not in working directory")
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33 parser$add_argument("-o", "--output", default="pubmed_by_queries_output",
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34 help = "output file name. [default \"%(default)s\"]")
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35 parser$add_argument("-n", "--number", type="integer", default=5,
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36 help="Number of PMIDs (or abstracts) to save per ID. [default \"%(default)s\"]")
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37 parser$add_argument("-a", "--abstract", action="store_true", default=FALSE,
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38 help="if abstracts instead of PMIDs should be retrieved use --abstracts ")
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39 parser$add_argument("-k", "--key", type="character",
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40 help="if ncbi API key is available, add it to speed up the download of pubmed data")
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41 parser$add_argument("--install_packages", action="store_true", default=FALSE,
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42 help="If you want to auto install missing required packages.")
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43 args <- parser$parse_args()
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44
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45 MAX_WEB_TRIES = 100
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46
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47 data = read.delim(args$input, stringsAsFactors=FALSE)
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48
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49 id_col_index <- grep("ID_", names(data))
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50
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51 pubmed_data_in_table <- function(data, row, query, number, key, abstract){
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52 if (is.null(query)){print(data)}
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53 pubmed_search <- get_pubmed_ids(query, api_key = key)
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54
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55 if(as.numeric(pubmed_search$Count) == 0){
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56 cat("No PubMed result for the following query: ", query, "\n")
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57 return(data)
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58
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59 } else if (abstract == FALSE) { # fetch PMIDs
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60
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61 myPubmedURL <- paste("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?",
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62 "db=pubmed&retmax=", number, "&term=", pubmed_search$OriginalQuery, "&usehistory=n", sep = "")
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63 # get ids
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64 idXML <- c()
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65 for (i in 1:MAX_WEB_TRIES){
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66 tryCatch({
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67 IDconnect <- suppressWarnings(url(myPubmedURL, open = "rb", encoding = "UTF8"))
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68 idXML <- suppressWarnings(readLines(IDconnect, warn = FALSE, encoding = "UTF8"))
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69 suppressWarnings(close(IDconnect))
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70 break
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71 }, error = function(e) {
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72 print(paste('Error getting URL, sleeping',2*i,'seconds.'))
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73 print(e)
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74 Sys.sleep(time = 2*i)
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75 })
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76 }
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77
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78 PMIDs = c()
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79
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80 for (i in 1:length(idXML)) {
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81 if (grepl("^<Id>", idXML[i])) {
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82 pmid <- custom_grep(idXML[i], tag = "Id", format = "char")
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83 PMIDs <- c(PMIDs, as.character(pmid[1]))
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84 }
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85 }
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86
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87
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88 if(length(PMIDs)>0){
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parents:
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89 data[row,sapply(1:length(PMIDs),function(i){paste0("PMID_",i)})] <- PMIDs
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
90 cat(length(PMIDs)," PMIDs for ",query, " are added in the table.", "\n")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
91 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
92
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
93 return(data)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
94
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
95 } else if (abstract == TRUE) { # fetch abstracts and title text
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
96
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
97 efetch_url = paste("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?",
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
98 "db=pubmed&WebEnv=", pubmed_search$WebEnv, "&query_key=", pubmed_search$QueryKey,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
99 "&retstart=", 0, "&retmax=", number,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
100 "&rettype=", "null","&retmode=", "xml", sep = "")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
101
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
102 api_key <- pubmed_search$APIkey
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
103 if (!is.null(api_key)) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
104 efetch_url <- paste(efetch_url, "&api_key=", api_key, sep = "")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
105 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
106
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
107 # initialize
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
108 out.data <- NULL
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
109 try_num <- 1
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
110 t_0 <- Sys.time()
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
111
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
112 # Try to fetch results
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
113 while(is.null(out.data)) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
114
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
115 # Timing check: kill at 3 min
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
116 if (try_num > 1){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
117 Sys.sleep(time = 2*try_num)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
118 cat("Problem to receive PubMed data or error is received. Please wait. Try number:",try_num,"\n")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
119 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
120
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
121 t_1 <- Sys.time()
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
122
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
123 if(as.numeric(difftime(t_1, t_0, units = "mins")) > 3){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
124 message("Killing the request! Something is not working. Please, try again later","\n")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
125 return(data)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
126 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
127
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
128 # ENTREZ server connect
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
129 out.data <- tryCatch({
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
130 tmpConnect <- suppressWarnings(url(efetch_url, open = "rb", encoding = "UTF8"))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
131 suppressWarnings(readLines(tmpConnect, warn = FALSE, encoding = "UTF8"))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
132 }, error = function(e) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
133 print(e)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
134 }, finally = {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
135 try(suppressWarnings(close(tmpConnect)), silent = TRUE)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
136 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
137
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
138 # Check if error
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
139 if (!is.null(out.data) &&
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
140 class(out.data) == "character" &&
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
141 grepl("<ERROR>", substr(paste(utils::head(out.data, n = 100), collapse = ""), 1, 250))) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
142 out.data <- NULL
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
143 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
144 try_num <- try_num + 1
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
145 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
146
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
147 if (is.null(out.data)) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
148 message("Killing the request! Something is not working. Please, try again later","\n")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
149 return(data)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
150 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
151
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
152 # process xml data
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
153 xml_data <- paste(out.data, collapse = "")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
154
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
155 # articles to list
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
156 xml_data <- strsplit(xml_data, "<PubmedArticle(>|[[:space:]]+?.*>)")[[1]][-1]
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
157 xml_data <- sapply(xml_data, function(x) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
158 #trim extra stuff at the end of the record
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
159 if (!grepl("</PubmedArticle>$", x))
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
160 x <- sub("(^.*</PubmedArticle>).*$", "\\1", x)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
161 # Rebuid XML structure and proceed
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
162 x <- paste("<PubmedArticle>", x)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
163 gsub("[[:space:]]{2,}", " ", x)},
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
164 USE.NAMES = FALSE, simplify = TRUE)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
165
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dlalgroup
parents:
diff changeset
166 #titles
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
167 titles = sapply(xml_data, function(x){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
168 x = custom_grep(x, tag="ArticleTitle", format="char")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
169 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
170 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
171 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
172 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
173 if (length(x) > 1){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
174 x <- paste(x, collapse = " ", sep = " ")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
175 } else if (length(x) < 1) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
176 x <- NA
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dlalgroup
parents:
diff changeset
177 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
178 x
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
179 },
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
180 USE.NAMES = FALSE, simplify = TRUE)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
181
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
182 # abstracts
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dlalgroup
parents:
diff changeset
183 abstract.text = sapply(xml_data, function(x){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
184 custom_grep(x, tag="AbstractText", format="char")},
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
185 USE.NAMES = FALSE, simplify = TRUE)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
186
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
187 abstracts <- sapply(abstract.text, function(x){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
188 if (length(x) > 1){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
189 x <- paste(x, collapse = " ", sep = " ")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
190 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
191 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
192 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
193 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
194 } else if (length(x) < 1) {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
195 x <- NA
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
196 } else {
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
197 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
198 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
199 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
200 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
201 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
202 x
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
203 },
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
204 USE.NAMES = FALSE, simplify = TRUE)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
205
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
206 #add title to abstracts
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
207 if (length(titles) == length(abstracts)){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
208 abstracts = paste(titles, abstracts)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
209 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
210
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
211 #add abstracts to data frame
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
212 if(length(abstracts)>0){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
213 data[row,sapply(1:length(abstracts),function(i){paste0("ABSTRACT_",i)})] <- abstracts
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
214 cat(length(abstracts)," abstracts for ",query, " are added in the table.", "\n")
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
215 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
216
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
217 return(data)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
218 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
219 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
220
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
221 for(i in 1:nrow(data)){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
222 data = tryCatch(pubmed_data_in_table(data= data,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
223 row= i,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
224 query= data[i,id_col_index],
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
225 number= args$number,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
226 key= args$key,
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
227 abstract= args$abstract), error=function(e){
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
228 print('main error')
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
229 print(e)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
230 Sys.sleep(5)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
231 })
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
232 }
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
233
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
234 write.table(data, args$output, append = FALSE, sep = '\t', row.names = FALSE, col.names = TRUE)
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
235
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
parents:
diff changeset
236