Mercurial > repos > proteore > proteore_kegg_pathways_coverage

annotate compute_kegg_pathways.R @ 0:8883a7173cba draft

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planemo upload commit 63302cb49d4f0f4dbc9ae141d20704822588f54e-dirty
author proteore
date Mon, 12 Nov 2018 10:59:49 -0500
parents
children 7004924a3686
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0
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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 = list[list != ""] #remove empty entry
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76 list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2")
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77 return(list)
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78 }
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79
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80 geneID_to_kegg <- function(vector,species){
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81 vector <- sapply(vector, function(x) paste(species,x,sep=":"),USE.NAMES = F)
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82 return (vector)
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83 }
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84
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85 kegg_mapping<- function(kegg_id_list,id_type,ref_ids) {
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86
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87 #convert to KEGG ID
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88 #if (id_type!="kegg-id"){
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89 # id_list <- unique(sapply(id_list, function(x) paste(id_type,":",x,sep=""),USE.NAMES = F))
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90 # if (length(id_list)>250){
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91 # id_list <- split(id_list, ceiling(seq_along(id_list)/250))
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92 # id_list <- sapply(id_list, function(x) keggConv("genes",x))
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93 # kegg_id_list <- unique(unlist(id_list))
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94 # } else {
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95 # kegg_id_list <- unique(keggConv("genes", id_list))
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96 # }
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97 #} else {
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98 # kegg_id_list <- unique(id_list)
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99 #}
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100
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101 #mapping
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102 map<-lapply(ref_ids, is.element, unique(kegg_id_list))
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103 names(map) <- sapply(names(map), function(x) gsub("path:","",x),USE.NAMES = FALSE) #remove the prefix "path:"
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104
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105 in.path<-sapply(map, function(x) length(which(x==TRUE)))
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106 tot.path<-sapply(map, length)
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107
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108 ratio <- (as.numeric(in.path[which(in.path!=0)])) / (as.numeric(tot.path[which(in.path!=0)]))
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109 ratio <- as.numeric(format(round(ratio*100, 2), nsmall = 2))
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110
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111 ##useful but LONG
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112 ## to do before : in step 1
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113 path.names<-names(in.path[which(in.path!=0)])
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114 name <- sapply(path.names, function(x) keggGet(x)[[1]]$NAME,USE.NAMES = FALSE)
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115
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116 res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)]))
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117 res <- res[order(as.numeric(res[,3]),decreasing = TRUE),]
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118 colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb KEGG genes IDs mapped in the pathway", "nb total of KEGG genes IDs present in the pathway")
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119
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120 return(res)
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121
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122 }
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123
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124 #get args from command line
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125 args <- get_args()
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126
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127 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_identification/args.Rda")
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128 #load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_identification/args.Rda")
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129
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130 ###setting variables
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131 header = str2bool(args$header)
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132 if (!is.null(args$id_list)) {id_list <- get_list_from_cp(args$id_list)}
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133 if (!is.null(args$input)) {
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134 csv <- read_file(args$input,header)
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135 ncol <- as.numeric(gsub("c", "" ,args$id_column))
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136 id_list <- as.vector(csv[,ncol])
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137 id_list <- id_list[which(!is.na(id_list))]
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138 }
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139 if (args$id_type == "ncbi-geneid") {
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140 id_list <- geneID_to_kegg(id_list,args$species)
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141 }
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142
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143
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144 #get pathways of species with associated KEGG ID genes
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145 pathways_list <- get_pathways_list(args$species)
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146
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147 #mapping on pathways
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148 res <- kegg_mapping(id_list,args$id_type,pathways_list)
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149 if (nrow(res) > as.numeric(args$nb_pathways)) { res <- res[1:args$nb_pathways,] }
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150
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151 write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
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152