Mercurial > repos > proteore > proteore_prot_features
annotate add_protein_features.R @ 16:7caa90759aba draft
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author | proteore |
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date | Fri, 28 Jun 2019 05:05:25 -0400 |
parents | 0116d444d21f |
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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() |