Mercurial > repos > proteore > proteore_kegg_pathways_coverage

annotate kegg_identification.R @ 6:042254fb1f8d draft default tip

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"planemo upload commit 151e7b469b231bbc43c4c39e8e836b05ab6d2253-dirty"
author proteore
date Mon, 17 May 2021 12:19:30 +0000
parents dc39f12f96d1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 options(warn = -1) #TURN OFF WARNINGS !!!!!!
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2
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3 suppressMessages(library(KEGGREST))
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4
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5 get_args <- function() {
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6
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7 ## Collect arguments
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8 args <- commandArgs(TRUE)
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9
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10 ## Default setting when no arguments passed
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11 if (length(args) < 1) {
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12 args <- c("--help")
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13 }
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14
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15 ## Help section
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16 if ("--help" %in% args) {
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17 cat("Pathview R script
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18 Arguments:
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19 --help Print this test
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20 --input tab file
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21 --id_list id list ',' separated
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22 --id_type type of input ids (kegg-id, uniprot_AC,geneID)
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23 --id_column number og column containg ids of interest
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24 --nb_pathways number of pathways to return
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25 --header boolean
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26 --output output path
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27 --species species used to get specific pathways(hsa,mmu,rno)
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28
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29 Example:
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30 Rscript keggrest.R --input='P31946,P62258' --id_type='uniprot'
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31 --id_column 'c1' --header TRUE \n\n")
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32
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33 q(save = "no")
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34 }
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35
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36 parseargs <- function(x) strsplit(sub("^--", "", x), "=")
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37 argsdf <- as.data.frame(do.call("rbind", parseargs(args)))
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38 args <- as.list(as.character(argsdf$V2))
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39 names(args) <- argsdf$V1
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40
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41 return(args)
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42 }
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43
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44 str2bool <- function(x) {
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45 if (any(is.element(c("t", "true"), tolower(x)))) {
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46 return(TRUE)
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47 }else if (any(is.element(c("f", "false"), tolower(x)))) {
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48 return(FALSE)
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49 }else {
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50 return(NULL)
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51 }
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52 }
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53
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54 read_file <- function(path, header) {
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55 file <- try(read.csv(path, header = header, sep = "\t",
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56 stringsAsFactors = FALSE, quote = "\"", check.names = F), silent = TRUE)
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57 if (inherits(file, "try-error")) {
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58 stop("File not found !")
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59 }else {
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60 return(file)
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61 }
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62 }
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63
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64 get_pathways_list <- function(species) {
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65 ##all available pathways for the species
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66 pathways <- keggLink("pathway", species)
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67 tot_path <- unique(pathways)
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68
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69 ##formating the dat into a list object
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70 ##key= pathway ID, value = genes of the pathway in the kegg format
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71 pathways_list <- sapply(tot_path, function(pathway)
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72 names(which(pathways == pathway)))
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73 return(pathways_list)
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74 }
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75
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76 get_list_from_cp <- function(list) {
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77 list <- strsplit(list, "[ \t\n]+")[[1]]
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78 list <- gsub("[[:blank:]]|\u00A0|NA", "", list)
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79 list <- list[which(!is.na(list[list != ""]))] #remove empty entry
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80 list <- unique(gsub("-.+", "", list))
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81 #Remove isoform accession number (e.g. "-2")
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82 return(list)
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83 }
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84
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85 geneid_to_kegg <- function(vector, species) {
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86 vector <- sapply(vector, function(x) paste(species, x, sep = ":"),
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87 USE.NAMES = F)
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88 return(vector)
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89 }
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90
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91 to_keggid <- function(id_list, id_type) {
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92 if (id_type == "ncbi-geneid") {
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93 id_list <- unique(geneid_to_kegg(id_list, args$species))
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94 }else if (id_type == "uniprot") {
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95 id_list <- unique(sapply(id_list, function(x)
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96 paste(id_type, ":", x, sep = ""), USE.NAMES = F))
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97 if (length(id_list) > 250) {
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98 id_list <- split(id_list, ceiling(seq_along(id_list) / 250))
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99 id_list <- sapply(id_list, function(x) keggConv("genes", x))
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100 id_list <- unique(unlist(id_list))
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101 } else {
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102 id_list <- unique(keggConv("genes", id_list))
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103 }
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104 } else if (id_type == "kegg-id") {
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105 id_list <- unique(id_list)
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106 }
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107 return(id_list)
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108 }
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109
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110 #take data frame, return data frame
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111 split_ids_per_line <- function(line, ncol) {
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112
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113 #print (line)
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114 header <- colnames(line)
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115 line[ncol] <- gsub("[[:blank:]]|\u00A0", "", line[ncol])
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116
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117 if (length(unlist(strsplit(as.character(line[ncol]), ";"))) > 1) {
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118 if (length(line) == 1) {
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119 lines <- as.data.frame(unlist(strsplit(
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120 as.character(line[ncol]), ";")), stringsAsFactors = F)
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121 } else {
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122 if (ncol == 1) { #first column
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123 lines <- suppressWarnings(cbind(unlist(strsplit(
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124 as.character(line[ncol]), ";")), line[2:length(line)]))
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125 } else if (ncol == length(line)) { #last column
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126 lines <- suppressWarnings(cbind(line[1:ncol - 1],
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127 unlist(strsplit(as.character(line[ncol]), ";"))))
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128 } else {
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129 lines <- suppressWarnings(cbind(line[1:ncol - 1],
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130 unlist(strsplit(as.character(line[ncol]), ";"), use.names = F),
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131 line[(ncol + 1):length(line)]))
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132 }
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133 }
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134 colnames(lines) <- header
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135 return(lines)
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136 } else {
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137 return(line)
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138 }
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139 }
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140
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141 #create new lines if there's more than one id per cell in the columns in order
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142 #to have only one id per line
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143 one_id_one_line <- function(tab, ncol) {
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144
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145 if (ncol(tab) > 1) {
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146
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147 tab[, ncol] <- sapply(tab[, ncol], function(x) gsub("[[:blank:]]", "", x))
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148 header <- colnames(tab)
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149 res <- as.data.frame(matrix(ncol = ncol(tab), nrow = 0))
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150 for (i in seq_len(nrow(tab))) {
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151 lines <- split_ids_per_line(tab[i, ], ncol)
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152 res <- rbind(res, lines)
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153 }
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154 } else {
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155 res <- unlist(sapply(tab[, 1], function(x) strsplit(x, ";")), use.names = F)
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156 res <- data.frame(res[which(!is.na(res[res != ""]))], stringsAsFactors = F)
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157 colnames(res) <- colnames(tab)
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158 }
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159 return(res)
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160 }
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161
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162 kegg_mapping <- function(kegg_id_list, id_type, ref_ids) {
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163
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164 #mapping
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165 map <- lapply(ref_ids, is.element, unique(kegg_id_list))
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166 names(map) <- sapply(names(map), function(x) gsub("path:", "", x),
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167 USE.NAMES = FALSE) #remove the prefix "path:"
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168
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169 in_path <- sapply(map, function(x) length(which(x == TRUE)))
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170 tot_path <- sapply(map, length)
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171
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172 ratio <- (as.numeric(in_path[which(in_path != 0)])) /
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173 (as.numeric(tot_path[which(in_path != 0)]))
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174 ratio <- as.numeric(format(round(ratio * 100, 2), nsmall = 2))
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175
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176 ##useful but LONG
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177 ## to do before : in step 1
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178 path_names <- names(in_path[which(in_path != 0)])
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179 name <- sapply(path_names, function(x) keggGet(x)[[1]]$NAME,
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180 USE.NAMES = FALSE)
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181
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182 res <- data.frame(I(names(in_path[which(in_path != 0)])), I(name), ratio,
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183 as.numeric(in_path[which(in_path != 0)]),
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184 as.numeric(tot_path[which(in_path != 0)]))
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185 res <- res[order(as.numeric(res[, 3]), decreasing = TRUE), ]
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186 colnames(res) <- c("pathway_ID", "Description",
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187 "Ratio IDs mapped / total IDs (%)",
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188 "nb KEGG genes IDs mapped in the pathway",
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189 "nb total of KEGG genes IDs present in the pathway")
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190
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191 return(res)
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192
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193 }
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194
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195 #get args from command line
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196 args <- get_args()
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197
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198 ###setting variables
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199 header <- str2bool(args$header)
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200 if (!is.null(args$id_list)) {
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201 id_list <- get_list_from_cp(args$id_list)
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202 } #get ids from copy/paste input
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203 if (!is.null(args$input)) { #get ids from input file
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204 csv <- read_file(args$input, header)
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205 ncol <- as.numeric(gsub("c", "", args$id_column))
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206 csv <- one_id_one_line(csv, ncol)
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207 id_list <- as.vector(csv[, ncol])
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208 id_list <- unique(id_list[which(!is.na(id_list[id_list != ""]))])
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209 }
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210
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211 #convert to keggID if needed
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212 id_list <- to_keggid(id_list, args$id_type)
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213
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214 #get pathways of species with associated KEGG ID genes
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215 pathways_list <- get_pathways_list(args$species)
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216
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217 #mapping on pathways
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218 res <- kegg_mapping(id_list, args$id_type, pathways_list)
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219 if (nrow(res) > as.numeric(args$nb_pathways)) {
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220 res <- res[1:args$nb_pathways, ]
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221 }
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222
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223 write.table(res, file = args$output, quote = FALSE, sep = "\t",
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224 row.names = FALSE, col.names = TRUE)