Mercurial > repos > proteore > proteore_prot_features

annotate protein_features.R @ 0:b455ec3f4f33 draft

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planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
author proteore
date Mon, 12 Nov 2018 11:10:16 -0500
parents
children 2fc914ab92f5
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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.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=dim.data.frame(file)[2]}
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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
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75 # Get information from neXtProt
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76 get_nextprot_info <- function(nextprot,input,pc_features,localization,diseases_info){
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77 if(diseases_info){
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78 cols = c("NextprotID",pc_features,localization,"Diseases")
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79 } else {
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80 cols = c("NextprotID",pc_features,localization)
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81 }
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82
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83 cols=cols[cols!="None"]
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84 info = nextprot[match(input,nextprot$NextprotID),cols]
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85 return(info)
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86 }
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87
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88 protein_features = function() {
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89
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90 args <- get_args()
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91
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92 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda")
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93 #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda")
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94
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95 #setting variables
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96 inputtype = args$inputtype
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97 if (inputtype == "copy_paste") {
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98 input = get_list_from_cp(args$input)
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99 input = input[input!=""]
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100 } else if (inputtype == "file") {
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101 filename = args$input
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102 ncol = args$column
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103 # Check ncol
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104 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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105 stop("Please enter an integer for level")
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106 } else {
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107 ncol = as.numeric(gsub("c", "", ncol))
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108 }
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109
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110 header = str2bool(args$header)
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111 file = read_file(filename, header) # Get file content
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112 input = sapply(file[,ncol],function(x) strsplit(as.character(x),";")[[1]][1],USE.NAMES = F) # Extract Protein IDs list
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113 if (args$type == "NextprotID" && ! "NextprotID" %in% colnames(file)) { colnames(file)[ncol] <- "NextprotID"
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114 } else if (args$type == "NextprotID" && "NextprotID" %in% colnames(file) && match("NextprotID",colnames(file))!=ncol ) {
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115 colnames(file)[match("NextprotID",colnames(file))] <- "old_NextprotID"
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116 colnames(file)[ncol] = "NextprotID"
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117 }
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118 }
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119
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120 # Read reference file
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121 nextprot = read_file(args$nextprot,T)
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122
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123 # Parse arguments
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124 id_type = args$type
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125 pc_features = strsplit(args$pc_features, ",")[[1]]
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126 localization = strsplit(args$localization, ",")[[1]]
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127 diseases_info = str2bool(args$diseases_info)
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128 output = args$output
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129
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130 # Change the sample ids if they are Uniprot_AC ids to be able to match them with
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131 # Nextprot data
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132 if (id_type=="Uniprot_AC"){
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133 NextprotID = gsub("^","NX_",input)
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134 if (inputtype == "file" && "NextprotID" %in% colnames(file)){colnames(file)[match("NextprotID",colnames(file))] <- "old_NextprotID"}
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135 file = cbind(file,NextprotID)
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136 } else if (id_type=="NextprotID") {
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137 if (inputtype == "file") {
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138 NextprotID = file$NextprotID
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139 } else {
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140 NextprotID = input
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141 }
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142 }
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143
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144 # Select user input protein ids in nextprot
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145 if ((length(NextprotID[NextprotID %in% nextprot[,1]]))==0){
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146 write.table("None of the input ids can be found in Nextprot",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
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147 } else {
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148 res <- get_nextprot_info(nextprot,NextprotID,pc_features,localization,diseases_info)
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149
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150 # Write output
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151 if (inputtype == "copy_paste") {
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152 if (id_type=="Uniprot_AC"){
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153 output_content = cbind(input, res)
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154 colnames(output_content)[1] = id_type
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155 }
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156 if ("res" %in% colnames(output_content)){colnames(output_content)[which(colnames(output_content)=="res")] = "NexprotID" } #if no features are selected
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157 } else if (inputtype == "file") {
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158 res = res[!duplicated(res$NextprotID),]
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159 output_content = merge(file, res,by="NextprotID",incomparables = NA,all.x=T)
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160 output_content = order_columns(output_content,ncol,id_type,file)
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161 }
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162 output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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163 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
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164 }
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165
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166 }
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167 protein_features()