Mercurial > repos > iuc > pmids_to_pubtator_matrix

annotate text_to_wordmatrix.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
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1 #!/usr/bin/env Rscript
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2 # tool: text_to_wordmatrix
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3 #
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4 #The tool extracts the most frequent words per entity (per row). Text of columns starting with "ABSTRACT" or "TEXT" are considered.
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5 #All extracted terms are used to generate a word matrix with rows = entities and columns = extracted words.
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6 #The resulting matrix is binary with 0= word not present in abstracts of entity and 1= word present in abstracts of entity.
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7 #
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8 #Input: Output of "pubmed_by_queries" or "abstracts_by_pmids", or tab-delimited table with entities in column called “ID_<name>”,
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9 #e.g. “ID_genes” and text in columns starting with "ABSTRACT" or "TEXT".
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10 #
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11 #Output: Binary matrix with rows = entities and columns = extracted words.
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12 #
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13 #usage: text_to_wordmatrix.R [-h] [-i INPUT] [-o OUTPUT] [-n NUMBER] [-r] [-l] [-w] [-s] [-p]
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14 #
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15 # optional arguments:
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16 # -h, --help show help message
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17 # -i INPUT, --input INPUT input file name. add path if file is not in working directory
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18 # -o OUTPUT, --output OUTPUT output file name. [default "text_to_wordmatrix_output"]
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19 # -n NUMBER, --number NUMBER number of most frequent words that should be extracted [default "50"]
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20 # -r, --remove_num remove any numbers in text
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21 # -l, --lower_case by default all characters are translated to lower case. otherwise use -l
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22 # -w, --remove_stopwords by default a set of english stopwords (e.g., "the" or "not") are removed. otherwise use -w
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23 # -s, --stemDoc apply Porter"s stemming algorithm: collapsing words to a common root to aid comparison of vocabulary
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24 # -p, --plurals by default words in plural and singular are merged to the singular form. otherwise use -p
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25
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26 if ("--install_packages" %in% commandArgs()) {
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27 print("Installing packages")
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28 if (!require("argparse")) install.packages("argparse", repo = "http://cran.rstudio.com/");
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29 if (!require("PubMedWordcloud")) install.packages("PubMedWordcloud", repo = "http://cran.rstudio.com/");
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30 if (!require("SnowballC")) install.packages("SnowballC", repo = "http://cran.rstudio.com/");
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31 if (!require("textclean")) install.packages("textclean", repo = "http://cran.rstudio.com/");
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32 if (!require("SemNetCleaner")) install.packages("SemNetCleaner", repo = "http://cran.rstudio.com/");
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33 if (!require("stringi")) install.packages("stringi", repo = "http://cran.rstudio.com/");
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34 if (!require("stringr")) install.packages("stringr", repo = "http://cran.rstudio.com/");
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35 }
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36
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37 suppressPackageStartupMessages(library("argparse"))
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38 suppressPackageStartupMessages(library("PubMedWordcloud"))
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39 suppressPackageStartupMessages(library("SnowballC"))
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40 suppressPackageStartupMessages(library("SemNetCleaner"))
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41 suppressPackageStartupMessages(library("textclean"))
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42 suppressPackageStartupMessages(library("stringi"))
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43 suppressPackageStartupMessages(library("stringr"))
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44
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45 parser <- ArgumentParser()
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46 parser$add_argument("-i", "--input",
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47 help = "input fie name. add path if file is not in workind directory")
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48 parser$add_argument("-o", "--output", default = "text_to_wordmatrix_output",
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49 help = "output file name. [default \"%(default)s\"]")
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50 parser$add_argument("-n", "--number", type = "integer", default = 50, choices = seq(1, 500), metavar = "{0..500}",
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51 help = "number of most frequent words used per ID in word matrix [default \"%(default)s\"]")
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52 parser$add_argument("-r", "--remove_num", action = "store_true", default = FALSE,
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53 help = "remove any numbers in text")
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54 parser$add_argument("-l", "--lower_case", action = "store_false", default = TRUE,
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55 help = "by default all characters are translated to lower case. otherwise use -l")
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56 parser$add_argument("-w", "--remove_stopwords", action = "store_false", default = TRUE,
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57 help = "by default a set of English stopwords (e.g., 'the' or 'not') are removed. otherwise use -s")
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58 parser$add_argument("-s", "--stemDoc", action = "store_true", default = FALSE,
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59 help = "apply Porter's stemming algorithm: collapsing words to a common root to aid comparison of vocabulary")
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60 parser$add_argument("-p", "--plurals", action = "store_false", default = TRUE,
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61 help = "by default words in plural and singular are merged to the singular form. otherwise use -p")
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62 parser$add_argument("--install_packages", action = "store_true", default = FALSE,
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63 help = "If you want to auto install missing required packages.")
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64
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65 args <- parser$parse_args()
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67
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68 data <- read.delim(args$input, stringsAsFactors = FALSE, header = TRUE, sep = "\t")
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69 word_matrix <- data.frame()
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70
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71 text_cols_index <- grep(c("ABSTRACT|TEXT"), names(data))
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72
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73 for (row in seq(nrow(data))) {
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74 top_words <- cleanAbstracts(abstracts = data[row, text_cols_index],
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75 rmNum = args$remove_num,
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76 tolw = args$lower_case,
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77 rmWords = args$remove_stopwords,
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78 stemDoc = args$stemDoc)
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79
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80 top_words$word <- as.character(top_words$word)
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81
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82 cat("Most frequent words for row", row, " are extracted.", "\n")
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83
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84 if (args$plurals == TRUE) {
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85 top_words$word <- sapply(top_words$word, function(x) {
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86 singularize(x)
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87 })
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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88 top_words <- aggregate(freq~word, top_words, sum)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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89 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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90
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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91 top_words <- top_words[order(top_words$freq, decreasing = TRUE), ]
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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92 top_words$word <- as.character(top_words$word)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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93
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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94 number_extract <- min(args$number, nrow(top_words))
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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95 word_matrix[row, sapply(1:number_extract, function(x) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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96 paste0(top_words$word[x])
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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97 })] <- top_words$freq[1:number_extract]
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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98 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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99
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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100 word_matrix <- as.matrix(word_matrix)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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101 word_matrix[is.na(word_matrix)] <- 0
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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102 word_matrix <- (word_matrix > 0) * 1 #binary matrix
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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103
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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104 cat("A matrix with ", nrow(word_matrix), " rows and ", ncol(word_matrix), "columns is generated.", "\n")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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105
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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106 write.table(word_matrix, args$output, row.names = FALSE, sep = "\t", quote = FALSE)