Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

annotate add_expression_HPA.R @ 12:f8d3a8a2f2e5 draft

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"planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
author proteore
date Thu, 23 Jan 2020 10:44:39 +0000
parents 07858c6dbbff
children 8ee4cfdc1a92
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 stopQuietly <- function(...) {
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23 blankMsg <- sprintf("\r%s\r", paste(rep(" ", getOption("width")-1L), collapse=" "));
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24 stop(simpleError(blankMsg));
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25 } # stopQuietly()
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26
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27 check_ensembl_geneids <- function(vector,type) {
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28 ensembl_geneid_pattern = "^ENS[A-Z]+[0-9]{11}$|^[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?$|^CG[0-9]+$|^[A-Z0-9]+[.][0-9]+$|^YM[A-Z][0-9]{3}[a-z][0-9]$"
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29 res = grepl(ensembl_geneid_pattern,vector)
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30 if (all(!res)){
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31 cat("No Ensembl geneIDs found in entered ids")
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32 stopQuietly()
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33 } else if (any(!res)) {
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34 cat(paste(sep="",collapse = " ",c(sum(!res, na.rm=TRUE),'IDs are not ENSG IDs, please check:\n')))
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35 not_geneids <- sapply(vector[which(!res)], function(x) paste(sep="",collapse = "",x,"\n"),USE.NAMES = F)
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36 cat(not_geneids)
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37 }
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38 }
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39
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40 add_expression = function(input, atlas, options) {
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41 input <- unique(input[!is.na(input)])
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42 input <- gsub("[[:blank:]]|\u00A0","",input)
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43 if (all(!input %in% atlas$Ensembl)) {
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44 return(NULL)
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45 } else {
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46 res = atlas[match(input,atlas$Ensembl),c("Ensembl",options)]
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47 res = res[which(!is.na(res[,1])),]
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48 row.names(res)=res[,1]
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49 res=res[2:ncol(res)]
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50 res <- as.data.frame(apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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51 return(res)
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52 }
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53 }
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54
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55 order_columns <- function (df,ncol){
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56 if (ncol==1){ #already at the right position
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57 return (df)
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58 } else {
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59 df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])]
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60 }
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61 return (df)
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62 }
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63
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64 #take data frame, return data frame
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65 split_ids_per_line <- function(line,ncol){
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66
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67 #print (line)
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68 header = colnames(line)
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69 line[ncol] = gsub("[[:blank:]]","",line[ncol])
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70
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71 if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
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72 if (length(line)==1 ) {
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73 lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
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74 } else {
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75 if (ncol==1) { #first column
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76 lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
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77 } else if (ncol==length(line)) { #last column
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78 lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
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79 } else {
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80 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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81 }
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82 }
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83 colnames(lines)=header
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84 return(lines)
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85 } else {
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86 return(line)
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87 }
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88 }
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89
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90 #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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91 one_id_one_line <-function(tab,ncol){
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92
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93 if (ncol(tab)>1){
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94
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95 tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
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96 header=colnames(tab)
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97 res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
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98 for (i in 1:nrow(tab) ) {
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99 lines = split_ids_per_line(tab[i,],ncol)
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100 res = rbind(res,lines)
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101 }
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102 }else {
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103 res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
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104 res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
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105 colnames(res)=colnames(tab)
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106 }
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107 return(res)
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108 }
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109
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110 get_args <- function(){
0
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111 args <- commandArgs(TRUE)
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112 if(length(args)<1) {
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113 args <- c("--help")
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114 }
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115
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116 # Help section
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117 if("--help" %in% args) {
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118 cat("Selection and Annotation HPA
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119 Arguments:
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120 --inputtype: type of input (list of id or filename)
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121 --input: either a file name (e.g : input.txt) or a list of blank-separated
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122 ENSG identifiers (e.g : ENSG00000283071 ENSG00000283072)
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123 --atlas: path to protein atlas file
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124 --column: the column number which you would like to apply...
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125 --header: true/false if your file contains a header
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126 --select: information from HPA to select, maybe:
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127 RNA.tissue.category,Reliability..IH.,Reliability..IF. (comma-separated)
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128 --output: text output filename \n")
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129 q(save="no")
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130 }
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131
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132 # Parse arguments
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133 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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134 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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135 args <- as.list(as.character(argsDF$V2))
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136 names(args) <- argsDF$V1
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137
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138 return(args)
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139 }
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140
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141 is_col_in_file <- function(file,ncol) {
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142 is_in_file = (ncol <= ncol(file) && ncol > 0)
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143 if (!is_in_file){
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144 cat(paste(sep = "", collapse = " ", c("Column",ncol,"not found in file") ))
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145 stopQuietly()
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146 }
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147 }
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148
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149 convert_to_previous_header <- function(options){
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150 header = c('Gene','description','Evidence','Antibody','RNA tissue specificity','Reliability (IH)','Reliability (IF)','Subcellular location','RNA tissue specific NX')
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151 names(header) = c('Gene','description','Evidence','Antibody','RNA tissue category','Reliability (IH)','Reliability (IF)','Subcellular location','RNA TS TPM')
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152 options = names(header[which(header %in% options)])
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153 return(options)
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154 }
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155
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156 main = function() {
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157
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158 args = get_args()
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159
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160 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
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161 #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
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162
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163 inputtype = args$inputtype
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164 if (inputtype == "copypaste") {
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165 ids = strsplit(args$input, "[ \t\n]+")[[1]]
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166 } else if (inputtype == "tabfile") {
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167 filename = args$input
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168 ncol = args$column
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169 # Check ncol
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170 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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171 stop("Please enter an integer for level")
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172 } else {
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173 ncol = as.numeric(gsub("c", "", ncol))
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174 }
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175 header = str2bool(args$header)
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176 file = read_file(filename, header)
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177 is_col_in_file(file,ncol)
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178 file = one_id_one_line(file,ncol)
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179 ids = unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
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180 ids = ids[which(!is.na(ids))]
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181 }
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182 check_ensembl_geneids(ids)
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183
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184 # Read protein atlas
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185 protein_atlas = read_file(args$atlas, T)
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186
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187 # Add expression
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188 output = args$output
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189 options = strsplit(args$select, ",")[[1]]
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190 if (tail(unlist(strsplit(args$atlas,"/")),1) == "HPA_full_atlas_23-10-2018.tsv"){ options = convert_to_previous_header(options)}
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191 res = add_expression(ids, protein_atlas, options)
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192
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193 # Write output
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194 if (is.null(res)) {
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195 write.table("None of the ENSG ids entered can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
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196 } else {
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197 if (inputtype == "copypaste") {
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198 ids <- data.frame(ids)
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199 output_content = merge(ids,res,by.x=1,by.y="row.names",incomparables = NA, all.x=T)
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200 colnames(output_content)[1] = "Ensembl"
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201 } else if (inputtype == "tabfile") {
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202 output_content = merge(file, res, by.x=ncol, by.y="row.names", incomparables = NA, all.x=T)
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203 output_content = order_columns(output_content,ncol)
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204 }
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205 output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))
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206 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
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207 }
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208 }
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209
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210 main()