Mercurial > repos > proteore > proteore_prot_features

annotate protein_features.R @ 2:9525c7c2d5d6 draft

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planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
author proteore
date Thu, 06 Dec 2018 05:25:41 -0500
parents 2fc914ab92f5
children 7746af0f8209
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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.table(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 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
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8 return(file)
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9 }
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10 }
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11
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12 order_columns <- function (df,ncol,id_type,file){
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13 if (id_type=="Uniprot_AC"){ncol=ncol(file)}
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14 if (ncol==1){ #already at the right position
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15 return (df)
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16 } else {
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17 df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])]
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18 }
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19 return (df)
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20 }
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21
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22 get_list_from_cp <-function(list){
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23 list = strsplit(list, "[ \t\n]+")[[1]]
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24 list = list[list != ""] #remove empty entry
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25 list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2")
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26 return(list)
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27 }
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28
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29 get_args <- function(){
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30
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31 ## Collect arguments
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32 args <- commandArgs(TRUE)
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33
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34 ## Default setting when no arguments passed
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35 if(length(args) < 1) {
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36 args <- c("--help")
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37 }
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38
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39 ## Help section
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40 if("--help" %in% args) {
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41 cat("Selection and Annotation HPA
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42 Arguments:
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43 --inputtype: type of input (list of id or filename)
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44 --input: input
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45 --nextprot: path to nextprot information 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 --type: the type of input IDs (Uniprot_AC/EntrezID)
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49 --pc_features: IsoPoint,SeqLength,MW
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50 --localization: Chr,SubcellLocations
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51 --diseases_info: Diseases
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52 --output: text output filename \n")
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53
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54 q(save="no")
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55 }
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56
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57 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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58 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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59 args <- as.list(as.character(argsDF$V2))
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60 names(args) <- argsDF$V1
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61
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62 return(args)
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63 }
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64
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65 str2bool <- function(x){
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66 if (any(is.element(c("t","true"),tolower(x)))){
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67 return (TRUE)
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68 }else if (any(is.element(c("f","false"),tolower(x)))){
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69 return (FALSE)
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70 }else{
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71 return(NULL)
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72 }
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73 }
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74
1
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75 #take data frame, return data frame
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76 split_ids_per_line <- function(line,ncol){
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77
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78 #print (line)
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79 header = colnames(line)
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80 line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol])
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81
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82 if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
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83 if (length(line)==1 ) {
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84 lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
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85 } else {
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86 if (ncol==1) { #first column
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87 lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
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88 } else if (ncol==length(line)) { #last column
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89 lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
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90 } else {
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91 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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92 }
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93 }
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94 colnames(lines)=header
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95 return(lines)
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96 } else {
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97 return(line)
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98 }
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99 }
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100
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101 #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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102 one_id_one_line <-function(tab,ncol){
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103
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104 if (ncol(tab)>1){
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105
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106 tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
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107 header=colnames(tab)
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108 res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
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109 for (i in 1:nrow(tab) ) {
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110 lines = split_ids_per_line(tab[i,],ncol)
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111 res = rbind(res,lines)
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112 }
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113 }else {
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114 res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
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115 res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
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116 colnames(res)=colnames(tab)
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117 }
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118 return(res)
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119 }
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120
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121 # Get information from neXtProt
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122 get_nextprot_info <- function(nextprot,input,pc_features,localization,diseases_info){
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123 if(diseases_info){
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124 cols = c("NextprotID",pc_features,localization,"Diseases")
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125 } else {
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126 cols = c("NextprotID",pc_features,localization)
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127 }
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128
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129 cols=cols[cols!="None"]
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130 info = nextprot[match(input,nextprot$NextprotID),cols]
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131 return(info)
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132 }
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133
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134 protein_features = function() {
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135
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136 args <- get_args()
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137
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138 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda")
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139 #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda")
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140
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141 #setting variables
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142 inputtype = args$inputtype
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143 if (inputtype == "copy_paste") {
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144 input = get_list_from_cp(args$input)
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145 input = input[which(!is.na(input[input!=""]))]
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146 ncol=1
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147 } else if (inputtype == "file") {
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148 filename = args$input
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149 ncol = args$column
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150 # Check ncol
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151 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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152 stop("Please enter an integer for level")
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153 } else {
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154 ncol = as.numeric(gsub("c", "", ncol))
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155 }
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156
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157 header = str2bool(args$header)
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158 file = read_file(filename, header) # Get file content
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159 if (any(grep(";",file[,ncol]))) {file = one_id_one_line(file,ncol)}
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160 input = sapply(file[,ncol],function(x) strsplit(as.character(x),";")[[1]][1],USE.NAMES = F) # Extract Protein IDs list
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161 if (args$type == "NextprotID" && ! "NextprotID" %in% colnames(file)) { colnames(file)[ncol] <- "NextprotID"
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162 } else if (args$type == "NextprotID" && "NextprotID" %in% colnames(file) && match("NextprotID",colnames(file))!=ncol ) {
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163 colnames(file)[match("NextprotID",colnames(file))] <- "old_NextprotID"
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164 colnames(file)[ncol] = "NextprotID"
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165 }
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166 }
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167
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168 # Read reference file
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169 nextprot = read_file(args$nextprot,T)
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170
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171 # Parse arguments
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172 id_type = args$type
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173 pc_features = strsplit(args$pc_features, ",")[[1]]
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174 localization = strsplit(args$localization, ",")[[1]]
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175 diseases_info = str2bool(args$diseases_info)
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176 output = args$output
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177
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178 # Change the sample ids if they are Uniprot_AC ids to be able to match them with
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179 # Nextprot data
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180 if (id_type=="Uniprot_AC"){
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181 NextprotID = gsub("^","NX_",input)
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182 if (inputtype == "file" && "NextprotID" %in% colnames(file)){
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183 colnames(file)[match("NextprotID",colnames(file))] <- "old_NextprotID"
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184 file = cbind(file,NextprotID)
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185 } else {
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186 file = data.frame(cbind(input,NextprotID))
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187 colnames(file)[1]="Uniprot-AC"
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188 }
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189 } else if (id_type=="NextprotID") {
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190 if (inputtype == "file") {
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191 NextprotID = file$NextprotID
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192 } else {
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193 NextprotID = input
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194 file=data.frame(NextprotID)
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195 }
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196 }
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197
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198 #Select user input protein ids in nextprot
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199 NextprotID = unique(NextprotID[which(!is.na(NextprotID[NextprotID!=""]))])
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200 if ((length(NextprotID[NextprotID %in% nextprot[,1]]))==0){
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201 write.table("None of the input ids can be found in Nextprot",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
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202 } else {
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203 res <- get_nextprot_info(nextprot,NextprotID,pc_features,localization,diseases_info)
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204 res = res[!duplicated(res$NextprotID),]
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205 output_content = merge(file, res,by="NextprotID",incomparables = NA,all.x=T)
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206 output_content = order_columns(output_content,ncol,id_type,file)
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207 output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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208 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
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209 }
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210
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211 }
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212 protein_features()