Mercurial > repos > proteore > proteore_prot_features_mouse

annotate add_protein_features_mouse.R @ 1:0679caefb2a3 draft default tip

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planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 04:01:38 -0400
parents b9f57cba3172
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 options(warn=-1) #TURN OFF WARNINGS !!!!!!
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2
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3 # Read file and return file content as data.frame
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4 order_columns <- function (df,ncol,file){
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5 if (ncol==1){ #already at the right position
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6 return (df)
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7 } else {
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8 df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])]
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9 }
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10 return (df)
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11 }
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12
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13 get_list_from_cp <-function(list){
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14 list = gsub(";","\t",list)
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15 list = strsplit(list, "[ \t\n]+")[[1]]
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16 list = gsub("NA","",list)
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17 list = list[list != ""] #remove empty entry
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18 list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2")
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19 return(list)
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20 }
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21
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22 check_ids <- function(vector,type) {
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23 uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
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24 entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
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25 if (type == "entrez")
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26 return(grepl(entrez_id,vector))
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27 else if (type == "uniprot") {
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28 return(grepl(uniprot_pattern,vector))
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29 }
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30 }
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31
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32 get_args <- function(){
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33
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34 ## Collect arguments
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35 args <- commandArgs(TRUE)
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36
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37 ## Default setting when no arguments passed
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38 if(length(args) < 1) {
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39 args <- c("--help")
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40 }
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41
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42 ## Help section
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43 if("--help" %in% args) {
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44 cat("Selection and Annotation HPA
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45 Arguments:
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46 --inputtype: type of input (list of id or filename)
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47 --input: input
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48 --uniprot_file: path to uniprot reference file
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49 --column: the column number which you would like to apply...
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50 --header: true/false if your file contains a header
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51 --pc_features: IsoPoint,SeqLength,MW
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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 #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_uniprot_info <- function(ids,pc_features,uniprot_file){
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123
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124 cols = c("Entry",pc_features)
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125 cols=cols[cols!="None"]
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126 info = uniprot_file[match(ids,uniprot_file$Entry),cols]
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127 colnames(info)[1]="UniProt-AC"
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128
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129 return(info)
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130 }
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131
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132 main <- function() {
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133
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134 args <- get_args()
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135
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136 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features_mouse/args.rda")
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137 #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features_mouse/args.rda")
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138
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139 #setting variables
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140 inputtype = args$inputtype
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141 if (inputtype == "copy_paste") {
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142 ids = get_list_from_cp(args$input)
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143
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144 #Check for UniProt-AC ids
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145 if (all(!check_ids(ids,'uniprot'))){
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146 stop ("No UniProt-AC found in ids.")
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147 } else if (any(!check_ids(ids,'uniprot'))) {
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148 print ('Some ids in ids are not uniprot-AC:')
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149 print (ids[which(!check_ids(ids,'uniprot'))])
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150 }
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151 file = data.frame(ids,stringsAsFactors = F)
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152 ncol=1
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153
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154 } else if (inputtype == "file") {
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155 filename = args$input
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156 ncol = args$column
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157 # Check ncol
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158 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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159 stop("Please enter an integer for level")
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160 } else {
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161 ncol = as.numeric(gsub("c", "", ncol))
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162 }
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163
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164 header = str2bool(args$header)
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165 file = read.table(filename, header = header , sep = "\t", fill = TRUE, stringsAsFactors = FALSE, quote="", check.names = F, comment.char = "") # Get file content
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166 if (any(grep(";",file[,ncol]))) {file = one_id_one_line(file,ncol)}
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167 ids=file[,ncol]
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168 }
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169
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170 # Read reference file
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171 uniprot_file <- read.table(args$uniprot_file, header = TRUE , sep = "\t", fill = TRUE,stringsAsFactors = FALSE, quote="", check.names = F, comment.char = "")
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172
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173 # Parse arguments
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174 pc_features = gsub("__ob__","[",gsub("__cb__","]",strsplit(args$pc_features, ",")[[1]]))
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175 output = args$output
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176
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177 #output file
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178 res <- get_uniprot_info(ids,pc_features,uniprot_file)
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179 res = res[!duplicated(res$`UniProt-AC`),]
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180 output_content = merge(file, res,by.x=ncol,by.y="UniProt-AC",incomparables = NA,all.x=T)
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181 output_content = order_columns(output_content,ncol,file)
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182 output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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183 write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
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184
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185 }
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186
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187 if(!interactive()) {
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188 main()
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189 }