Mercurial > repos > proteore > proteore_compute_kegg_pathways

annotate compute_kegg_pathways.R @ 4:7d8848c4dbb7 draft default tip

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planemo upload commit 229c140e131039467e2797f656d9acf916907dd7-dirty
author proteore
date Tue, 18 Sep 2018 09:54:58 -0400
parents 0d5c21cc29f7
children
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0
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1 library(KEGGREST)
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2
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3 get_args <- function(){
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4
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5 ## Collect arguments
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6 args <- commandArgs(TRUE)
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7
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8 ## Default setting when no arguments passed
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9 if(length(args) < 1) {
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10 args <- c("--help")
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11 }
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12
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13 ## Help section
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14 if("--help" %in% args) {
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15 cat("Pathview R script
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16 Arguments:
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17 --help Print this test
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18 --input tab file
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19 --id_list
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20 id list ',' separated
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21 --id_type type of input ids (uniprot_AC or geneID)
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22 --id_column number og column containg ids of interest
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23 --nb_pathways number of pathways to return
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24 --header boolean
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25 --output output path
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26 --ref ref file (l.hsa.gene.RData, l.hsa.up.RData, l.mmu.up.Rdata)
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27
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28 Example:
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29 Rscript keggrest.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE \n\n")
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30
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31 q(save="no")
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32 }
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33
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34 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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35 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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36 args <- as.list(as.character(argsDF$V2))
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37 names(args) <- argsDF$V1
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38
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39 return(args)
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40 }
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41
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42 args <- get_args()
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43
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44 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/compute_KEGG_pathways/args.Rda")
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45 #load("/home/dchristiany/proteore_project/ProteoRE/tools/compute_KEGG_pathways/args.Rda")
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46
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47 ##function arguments :
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48 ## id.ToMap = input from the user to map on the pathways = list of IDs
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49 ## idType : must be "UNIPROT" or "ENTREZ"
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50 ## org : for the moment can be "Hs" only. Has to evoluate to "Mm"
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51
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52 str2bool <- function(x){
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53 if (any(is.element(c("t","true"),tolower(x)))){
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54 return (TRUE)
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55 }else if (any(is.element(c("f","false"),tolower(x)))){
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56 return (FALSE)
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57 }else{
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58 return(NULL)
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59 }
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60 }
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61
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62
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63 read_file <- function(path,header){
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64 file <- try(read.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote=""),silent=TRUE)
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65 if (inherits(file,"try-error")){
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66 stop("File not found !")
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67 }else{
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68 return(file)
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69 }
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70 }
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71
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72 ID2KEGG.Mapping<- function(id.ToMap,ref) {
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73
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74 ref_ids = get(load(ref))
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75 map<-lapply(ref_ids, is.element, unique(id.ToMap))
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76 names(map) <- sapply(names(map), function(x) gsub("path:","",x),USE.NAMES = FALSE) #remove the prefix "path:"
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77
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78 in.path<-sapply(map, function(x) length(which(x==TRUE)))
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79 tot.path<-sapply(map, length)
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80
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81 ratio<-(as.numeric(in.path[which(in.path!=0)])) / (as.numeric(tot.path[which(in.path!=0)]))
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82 ratio <- as.numeric(format(round(ratio*100, 2), nsmall = 2))
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83
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84 ##useful but LONG
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85 ## to do before : in step 1
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86 path.names<-names(in.path[which(in.path!=0)])
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87 name <- sapply(path.names, function(x) keggGet(x)[[1]]$NAME,USE.NAMES = FALSE)
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88
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89 res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)]))
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90 res <- res[order(as.numeric(res[,3]),decreasing = TRUE),]
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91 colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb genes mapped in the pathway", "nb total genes present in the pathway")
0
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92
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93 return(res)
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94
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95 }
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96
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97 ###setting variables
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98 header = str2bool(args$header)
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99 if (!is.null(args$id_list)) {id_list <- strsplit(args$id_list,",")[[1]]}
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100 if (!is.null(args$input)) {
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101 csv <- read_file(args$input,header)
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102 ncol <- as.numeric(gsub("c", "" ,args$id_column))
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103 id_list <- as.vector(csv[,ncol])
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104 }
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105 id_type <- toupper(args$id_type)
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106
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107 #mapping on pathways
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108 res <- ID2KEGG.Mapping(id_list,args$ref)
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109 if (nrow(res) > as.numeric(args$nb_pathways)) { res <- res[1:args$nb_pathways,] }
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110
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111 write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
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112