Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

annotate add_expression_HPA.R @ 0:234d114cbe3a draft

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planemo upload commit 2ee714c3e3d1cce461125dbc041904e03ea8bac1-dirty
author proteore
date Mon, 12 Nov 2018 11:05:24 -0500
parents
children 03487ed0f458
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0
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1 # Read file and return file content as data.frame
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2 read_file <- function(path,header){
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3 file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE)
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4 if (inherits(file,"try-error")){
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5 stop("File not found !")
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6 }else{
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7 return(file)
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8 }
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9 }
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10
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11 #convert a string to boolean
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12 str2bool <- function(x){
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13 if (any(is.element(c("t","true"),tolower(x)))){
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14 return (TRUE)
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15 }else if (any(is.element(c("f","false"),tolower(x)))){
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16 return (FALSE)
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17 }else{
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18 return(NULL)
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19 }
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20 }
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21
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22 add_expression = function(input, atlas, options) {
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23 if (all(!input %in% atlas$Ensembl)) {
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24 return(NULL)
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25 } else {
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26 res = atlas[match(input,atlas$Ensembl),c("Ensembl",options)]
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27 res <- as.data.frame(apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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28 return(res)
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29 }
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30 }
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31
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32 main = function() {
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33 args <- commandArgs(TRUE)
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34 if(length(args)<1) {
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35 args <- c("--help")
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36 }
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37
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38 # Help section
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39 if("--help" %in% args) {
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40 cat("Selection and Annotation HPA
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41 Arguments:
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42 --inputtype: type of input (list of id or filename)
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43 --input: either a file name (e.g : input.txt) or a list of blank-separated
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44 ENSG identifiers (e.g : ENSG00000283071 ENSG00000283072)
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45 --atlas: path to protein atlas file
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46 --column: the column number which you would like to apply...
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47 --header: true/false if your file contains a header
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48 --select: information from HPA to select, maybe:
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49 RNA.tissue.category,Reliability..IH.,Reliability..IF. (comma-separated)
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50 --output: text output filename \n")
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51 q(save="no")
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52 }
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53
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54 # Parse arguments
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55 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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56 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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57 args <- as.list(as.character(argsDF$V2))
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58 names(args) <- argsDF$V1
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59
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60 save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
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61 #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
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62
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63 inputtype = args$inputtype
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64 if (inputtype == "copypaste") {
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65 input = strsplit(args$input, "[ \t\n]+")[[1]]
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66 } else if (inputtype == "tabfile") {
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67 filename = args$input
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68 ncol = args$column
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69 # Check ncol
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70 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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71 stop("Please enter an integer for level")
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72 } else {
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73 ncol = as.numeric(gsub("c", "", ncol))
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74 }
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75 header = str2bool(args$header)
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76 file = read_file(filename, header)
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77 input = unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
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78 }
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79
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80 # Read protein atlas
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81 protein_atlas = args$atlas
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82 protein_atlas = read_file(protein_atlas, T)
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83
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84 # Add expression
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85 output = args$output
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86 options = strsplit(args$select, ",")[[1]]
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87 res = add_expression(input, protein_atlas, options)
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88
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89
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90 # Write output
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91 if (is.null(res)) {
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92 write.table("None of the input ENSG ids are can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
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93 } else {
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94 if (inputtype == "copypaste") {
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95 output_content = cbind(as.matrix(input), res)
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96 colnames(output_content)[1] = "Ensembl"
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97 } else if (inputtype == "tabfile") {
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98 output_content = merge(file, res, by.x=ncol, by.y=1, incomparables = NA,all.x=T)
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99 output_content = output_content[order(output_content[,ncol],decreasing = T),]
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100 }
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101 output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))
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102 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
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103 }
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104 }
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105
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106 main()