Mercurial > repos > proteore > proteore_kegg_pathways_coverage

annotate kegg_identification.R @ 4:dc39f12f96d1 draft

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planemo upload commit 6854718828a7478905b41fb92d6f96ab41896e84-dirty
author proteore
date Tue, 14 May 2019 09:04:22 -0400
parents e7b3609160c5
children 042254fb1f8d
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3
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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' --id_column 'c1' --header TRUE \n\n")
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31
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32 q(save="no")
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33 }
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34
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35 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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36 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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37 args <- as.list(as.character(argsDF$V2))
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38 names(args) <- argsDF$V1
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39
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40 return(args)
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41 }
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42
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43 str2bool <- function(x){
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44 if (any(is.element(c("t","true"),tolower(x)))){
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45 return (TRUE)
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46 }else if (any(is.element(c("f","false"),tolower(x)))){
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47 return (FALSE)
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48 }else{
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49 return(NULL)
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50 }
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51 }
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52
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53 read_file <- function(path,header){
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54 file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE)
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55 if (inherits(file,"try-error")){
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56 stop("File not found !")
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57 }else{
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58 return(file)
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59 }
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60 }
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61
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62 get_pathways_list <- function(species){
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63 ##all available pathways for the species
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64 pathways <-keggLink("pathway", species)
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65 tot_path<-unique(pathways)
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66
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67 ##formating the dat into a list object
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68 ##key= pathway ID, value = genes of the pathway in the kegg format
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69 pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway)))
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70 return (pathways_list)
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71 }
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72
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73 get_list_from_cp <-function(list){
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74 list = strsplit(list, "[ \t\n]+")[[1]]
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75 list = gsub("[[:blank:]]|\u00A0|NA","",list)
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76 list = list[which(!is.na(list[list != ""]))] #remove empty entry
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77 list = unique(gsub("-.+", "", list)) #Remove isoform accession number (e.g. "-2")
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78 return(list)
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79 }
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80
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81 geneID_to_kegg <- function(vector,species){
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82 vector <- sapply(vector, function(x) paste(species,x,sep=":"),USE.NAMES = F)
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83 return (vector)
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84 }
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85
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86 to_keggID <- function(id_list,id_type){
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87 if (id_type == "ncbi-geneid") {
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88 id_list <- unique(geneID_to_kegg(id_list,args$species))
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89 } else if (id_type=="uniprot"){
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90 id_list <- unique(sapply(id_list, function(x) paste(id_type,":",x,sep=""),USE.NAMES = F))
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91 if (length(id_list)>250){
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92 id_list <- split(id_list, ceiling(seq_along(id_list)/250))
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93 id_list <- sapply(id_list, function(x) keggConv("genes",x))
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94 id_list <- unique(unlist(id_list))
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95 } else {
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96 id_list <- unique(keggConv("genes", id_list))
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97 }
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98 } else if (id_type=="kegg-id") {
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99 id_list <- unique(id_list)
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100 }
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101 return (id_list)
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102 }
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103
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104 #take data frame, return data frame
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105 split_ids_per_line <- function(line,ncol){
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106
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107 #print (line)
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108 header = colnames(line)
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109 line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol])
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110
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111 if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
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112 if (length(line)==1 ) {
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113 lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
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114 } else {
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115 if (ncol==1) { #first column
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116 lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
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117 } else if (ncol==length(line)) { #last column
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118 lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
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119 } else {
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120 lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)]))
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121 }
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122 }
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123 colnames(lines)=header
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124 return(lines)
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125 } else {
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126 return(line)
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127 }
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128 }
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129
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130 #create new lines if there's more than one id per cell in the columns in order to have only one id per line
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131 one_id_one_line <-function(tab,ncol){
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132
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133 if (ncol(tab)>1){
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134
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135 tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
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136 header=colnames(tab)
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137 res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
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138 for (i in 1:nrow(tab) ) {
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139 lines = split_ids_per_line(tab[i,],ncol)
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140 res = rbind(res,lines)
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141 }
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142 }else {
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143 res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
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144 res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
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145 colnames(res)=colnames(tab)
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146 }
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147 return(res)
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148 }
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149
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150 kegg_mapping<- function(kegg_id_list,id_type,ref_ids) {
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151
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152 #mapping
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153 map<-lapply(ref_ids, is.element, unique(kegg_id_list))
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154 names(map) <- sapply(names(map), function(x) gsub("path:","",x),USE.NAMES = FALSE) #remove the prefix "path:"
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155
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156 in.path<-sapply(map, function(x) length(which(x==TRUE)))
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157 tot.path<-sapply(map, length)
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158
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159 ratio <- (as.numeric(in.path[which(in.path!=0)])) / (as.numeric(tot.path[which(in.path!=0)]))
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160 ratio <- as.numeric(format(round(ratio*100, 2), nsmall = 2))
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161
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162 ##useful but LONG
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163 ## to do before : in step 1
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164 path.names<-names(in.path[which(in.path!=0)])
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165 name <- sapply(path.names, function(x) keggGet(x)[[1]]$NAME,USE.NAMES = FALSE)
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166
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167 res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)]))
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168 res <- res[order(as.numeric(res[,3]),decreasing = TRUE),]
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169 colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb KEGG genes IDs mapped in the pathway", "nb total of KEGG genes IDs present in the pathway")
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170
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171 return(res)
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172
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173 }
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174
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175 #get args from command line
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176 args <- get_args()
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177
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178 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_identification/args.Rda")
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179 #load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_identification/args.Rda")
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180
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181 ###setting variables
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182 header = str2bool(args$header)
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183 if (!is.null(args$id_list)) {id_list <- get_list_from_cp(args$id_list)} #get ids from copy/paste input
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184 if (!is.null(args$input)) { #get ids from input file
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185 csv <- read_file(args$input,header)
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186 ncol <- as.numeric(gsub("c", "" ,args$id_column))
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187 csv <- one_id_one_line(csv,ncol)
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188 id_list <- as.vector(csv[,ncol])
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189 id_list <- unique(id_list[which(!is.na(id_list[id_list!=""]))])
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190 }
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191
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192 #convert to keggID if needed
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193 id_list <- to_keggID(id_list,args$id_type)
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194
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195 #get pathways of species with associated KEGG ID genes
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196 pathways_list <- get_pathways_list(args$species)
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197
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198 #mapping on pathways
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199 res <- kegg_mapping(id_list,args$id_type,pathways_list)
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200 if (nrow(res) > as.numeric(args$nb_pathways)) { res <- res[1:args$nb_pathways,] }
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201
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202 write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
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203