Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

annotate add_expression_HPA.R @ 5:e919b55188ab draft

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planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
author proteore
date Wed, 02 Jan 2019 04:26:18 -0500
parents d7d2a4512059
children ea59f5750c51
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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 input <- unique(input[!is.na(input)])
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24 input <- gsub("[[:blank:]]|\u00A0","",input)
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25 if (all(!input %in% atlas$Ensembl)) {
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26 return(NULL)
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27 } else {
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28 res = atlas[match(input,atlas$Ensembl),c("Ensembl",options)]
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29 res = res[which(!is.na(res[,1])),]
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30 row.names(res)=res[,1]
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31 res=res[2:ncol(res)]
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32 res <- as.data.frame(apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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33 return(res)
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34 }
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35 }
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36
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37 order_columns <- function (df,ncol){
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38 if (ncol==1){ #already at the right position
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39 return (df)
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40 } else {
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41 df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])]
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42 }
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43 return (df)
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44 }
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45
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46 #take data frame, return data frame
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47 split_ids_per_line <- function(line,ncol){
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48
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49 #print (line)
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50 header = colnames(line)
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51 line[ncol] = gsub("[[:blank:]]","",line[ncol])
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52
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53 if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
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54 if (length(line)==1 ) {
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55 lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
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56 } else {
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57 if (ncol==1) { #first column
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58 lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
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59 } else if (ncol==length(line)) { #last column
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60 lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
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61 } else {
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62 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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63 }
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64 }
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65 colnames(lines)=header
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66 return(lines)
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67 } else {
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68 return(line)
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69 }
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70 }
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71
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72 #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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73 one_id_one_line <-function(tab,ncol){
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74
3
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75 if (ncol(tab)>1){
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76
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77 tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
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78 header=colnames(tab)
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79 res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
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80 for (i in 1:nrow(tab) ) {
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81 lines = split_ids_per_line(tab[i,],ncol)
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82 res = rbind(res,lines)
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83 }
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84 }else {
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85 res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
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86 res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
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87 colnames(res)=colnames(tab)
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88 }
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89 return(res)
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90 }
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91
0
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92 main = function() {
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93 args <- commandArgs(TRUE)
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94 if(length(args)<1) {
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95 args <- c("--help")
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96 }
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97
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98 # Help section
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99 if("--help" %in% args) {
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100 cat("Selection and Annotation HPA
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101 Arguments:
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102 --inputtype: type of input (list of id or filename)
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103 --input: either a file name (e.g : input.txt) or a list of blank-separated
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104 ENSG identifiers (e.g : ENSG00000283071 ENSG00000283072)
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105 --atlas: path to protein atlas file
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106 --column: the column number which you would like to apply...
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107 --header: true/false if your file contains a header
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108 --select: information from HPA to select, maybe:
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109 RNA.tissue.category,Reliability..IH.,Reliability..IF. (comma-separated)
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110 --output: text output filename \n")
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111 q(save="no")
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112 }
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113
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114 # Parse arguments
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115 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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116 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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117 args <- as.list(as.character(argsDF$V2))
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118 names(args) <- argsDF$V1
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119
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120 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
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121 #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
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122
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123 inputtype = args$inputtype
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124 if (inputtype == "copypaste") {
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125 input = strsplit(args$input, "[ \t\n]+")[[1]]
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126 } else if (inputtype == "tabfile") {
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127 filename = args$input
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128 ncol = args$column
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129 # Check ncol
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130 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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131 stop("Please enter an integer for level")
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132 } else {
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133 ncol = as.numeric(gsub("c", "", ncol))
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134 }
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135 header = str2bool(args$header)
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136 file = read_file(filename, header)
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137 file = one_id_one_line(file,ncol)
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138 input = unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
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139 input = input[which(!is.na(input))]
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140 }
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141
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142 # Read protein atlas
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143 protein_atlas = args$atlas
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144 protein_atlas = read_file(protein_atlas, T)
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145
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146 # Add expression
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147 output = args$output
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148 options = strsplit(args$select, ",")[[1]]
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149 res = add_expression(input, protein_atlas, options)
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150
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151 # Write output
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152 if (is.null(res)) {
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153 write.table("None of the input ENSG ids are can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
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154 } else {
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155 if (inputtype == "copypaste") {
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156 input <- data.frame(input)
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157 output_content = merge(input,res,by.x=1,by.y="row.names",incomparables = NA, all.x=T)
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158 colnames(output_content)[1] = "Ensembl"
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159 } else if (inputtype == "tabfile") {
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160 output_content = merge(file, res, by.x=ncol, by.y="row.names", incomparables = NA, all.x=T)
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161 output_content = order_columns(output_content,ncol)
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162 }
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163 output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))
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164 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
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165 }
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166 }
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167
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168 main()