Mercurial > repos > proteore > proteore_prot_features

annotate add_protein_features.R @ 14:564e620ba3cb draft

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planemo upload commit e8aae7c385ce83f4ae7494d53b1c0190e3ef6f9a-dirty
author proteore
date Tue, 14 May 2019 09:43:07 -0400
parents aca66c3b8fbb
children bdbc7620e804
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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 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 = gsub(";","\t",list)
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24 list = strsplit(list, "[ \t\n]+")[[1]]
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25 list = gsub("NA","",list)
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26 list = list[list != ""] #remove empty entry
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27 list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2")
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28 return(list)
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29 }
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30
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31 get_args <- function(){
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32
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33 ## Collect arguments
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34 args <- commandArgs(TRUE)
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35
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36 ## Default setting when no arguments passed
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37 if(length(args) < 1) {
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38 args <- c("--help")
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39 }
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40
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41 ## Help section
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42 if("--help" %in% args) {
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43 cat("Selection and Annotation HPA
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44 Arguments:
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45 --inputtype: type of input (list of id or filename)
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46 --input: input
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47 --nextprot: path to nextprot information file
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48 --column: the column number which you would like to apply...
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49 --header: true/false if your file contains a header
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50 --type: the type of input IDs (Uniprot_AC/EntrezID)
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51 --pc_features: IsoPoint,SeqLength,MW
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52 --localization: Chr,SubcellLocations
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53 --diseases_info: Diseases
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54 --output: text output filename \n")
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55
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56 q(save="no")
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57 }
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58
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59 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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60 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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61 args <- as.list(as.character(argsDF$V2))
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62 names(args) <- argsDF$V1
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63
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64 return(args)
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65 }
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66
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67 str2bool <- function(x){
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68 if (any(is.element(c("t","true"),tolower(x)))){
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69 return (TRUE)
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70 }else if (any(is.element(c("f","false"),tolower(x)))){
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71 return (FALSE)
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72 }else{
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73 return(NULL)
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74 }
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75 }
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76
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77 #take data frame, return data frame
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78 split_ids_per_line <- function(line,ncol){
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79
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80 #print (line)
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81 header = colnames(line)
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82 line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol])
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83
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84 if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
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85 if (length(line)==1 ) {
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86 lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
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87 } else {
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88 if (ncol==1) { #first column
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89 lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
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90 } else if (ncol==length(line)) { #last column
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91 lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
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92 } else {
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93 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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94 }
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95 }
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96 colnames(lines)=header
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97 return(lines)
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98 } else {
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99 return(line)
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100 }
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101 }
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102
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103 #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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104 one_id_one_line <-function(tab,ncol){
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105
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106 if (ncol(tab)>1){
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107
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108 tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
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109 header=colnames(tab)
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110 res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
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111 for (i in 1:nrow(tab) ) {
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112 lines = split_ids_per_line(tab[i,],ncol)
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113 res = rbind(res,lines)
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114 }
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115 }else {
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116 res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
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117 res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
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118 colnames(res)=colnames(tab)
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119 }
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120 return(res)
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121 }
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122
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123 # Get information from neXtProt
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124 get_nextprot_info <- function(nextprot,input,pc_features,localization,diseases_info){
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125 if(diseases_info){
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126 cols = c("NextprotID",pc_features,localization,"Diseases")
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127 } else {
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128 cols = c("NextprotID",pc_features,localization)
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129 }
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130
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131 cols=cols[cols!="None"]
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132 info = nextprot[match(input,nextprot$NextprotID),cols]
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133 return(info)
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134 }
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135
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136 protein_features = function() {
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137
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138 args <- get_args()
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139
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140 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features/args.rda")
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141 #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features/args.rda")
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142
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143 #setting variables
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144 inputtype = args$inputtype
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145 if (inputtype == "copy_paste") {
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146 input = get_list_from_cp(args$input)
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147 file = data.frame(input,stringsAsFactors = F)
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148 ncol=1
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149 } else if (inputtype == "file") {
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150 filename = args$input
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151 ncol = args$column
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152 # Check ncol
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153 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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154 stop("Please enter an integer for level")
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155 } else {
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156 ncol = as.numeric(gsub("c", "", ncol))
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157 }
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158
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159 header = str2bool(args$header)
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160 file = read_file(filename, header) # Get file content
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161 if (any(grep(";",file[,ncol]))) {file = one_id_one_line(file,ncol)}
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162 if (args$type == "NextprotID" && ! "NextprotID" %in% colnames(file)) { colnames(file)[ncol] <- "NextprotID"
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163 } else if (args$type == "NextprotID" && "NextprotID" %in% colnames(file) && match("NextprotID",colnames(file))!=ncol ) {
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164 colnames(file)[match("NextprotID",colnames(file))] <- "old_NextprotID"
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165 colnames(file)[ncol] = "NextprotID"
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166 }
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167 }
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168
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169 # Read reference file
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170 nextprot = read_file(args$nextprot,T)
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171
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172 # Parse arguments
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173 id_type = args$type
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174 pc_features = strsplit(args$pc_features, ",")[[1]]
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175 localization = strsplit(args$localization, ",")[[1]]
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176 diseases_info = str2bool(args$diseases_info)
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177 output = args$output
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178
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179 # Change the sample ids if they are Uniprot_AC ids to be able to match them with
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180 # Nextprot data
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181 if (id_type=="Uniprot_AC"){
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182 NextprotID = gsub("^NX_$","",gsub("^","NX_",file[,ncol]))
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183 file = cbind(file,NextprotID)
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184 if (inputtype=="copy_paste") {colnames(file)[1]="Uniprot-AC"}
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185 ncol=ncol(file)
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186 }
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187 NextprotID = file[,ncol]
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188
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189 #Select user input protein ids in nextprot
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190 #NextprotID = unique(NextprotID[which(!is.na(NextprotID[NextprotID!=""]))])
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191 if (all(!NextprotID %in% nextprot[,1])){
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192 write.table("None of the input ids can be found in Nextprot",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
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193 } else {
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194 res <- get_nextprot_info(nextprot,NextprotID,pc_features,localization,diseases_info)
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195 res = res[!duplicated(res$NextprotID),]
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196 output_content = merge(file, res,by.x=ncol,by.y="NextprotID",incomparables = NA,all.x=T)
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197 output_content = order_columns(output_content,ncol,id_type,file)
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198 if (id_type=="Uniprot_AC"){output_content = output_content[,-which(colnames(output_content)=="NextprotID")]} #remove nextprotID column
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199 output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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200 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
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201 }
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202
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203 }
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204 protein_features()