Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.R @ 8:386145573c19 draft

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planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b
author proteore
date Tue, 18 Dec 2018 09:54:57 -0500
parents 3e138d54c105
children 948fecb6a40b
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1 options(warn=-1) #TURN OFF WARNINGS !!!!!!
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2
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3 # Load necessary libraries
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4 suppressMessages(library(goProfiles,quietly = TRUE))
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6 # Read file and return file content as data.frame
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7 read_file <- function(path,header){
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8 file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE)
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9 if (inherits(file,"try-error")){
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10 stop("File not found !")
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11 }else{
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12 return(file)
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13 }
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14 }
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15
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16 #convert a string to boolean
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17 str2bool <- function(x){
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18 if (any(is.element(c("t","true"),tolower(x)))){
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19 return (TRUE)
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20 }else if (any(is.element(c("f","false"),tolower(x)))){
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21 return (FALSE)
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22 }else{
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23 return(NULL)
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24 }
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25 }
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26
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27 check_ids <- function(vector,type) {
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28 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})$"
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29 entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
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30 if (type == "Entrez"){
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31 return(grepl(entrez_id,vector))
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32 } else if (type == "UniProt") {
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33 return(grepl(uniprot_pattern,vector))
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34 }
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35 }
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36
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37 getprofile = function(ids, id_type, level, duplicate,species) {
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38 ####################################################################
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39 # Arguments
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40 # - ids: list of input IDs
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41 # - id_type: type of input IDs (UniProt/ENTREZID)
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42 # - level
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43 # - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE)
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44 # - species
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45 ####################################################################
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46
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47 library(species, character.only = TRUE, quietly = TRUE)
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48
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49 if (species=="org.Hs.eg.db"){
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50 package=org.Hs.eg.db
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51 } else if (species=="org.Mm.eg.db"){
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52 package=org.Mm.eg.db
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53 } else if (species=="org.Rn.eg.db"){
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54 package=org.Rn.eg.db
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55 }
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56
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57 # Check if level is number
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58 if (! as.numeric(level) %% 1 == 0) {
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59 stop("Please enter an integer for level")
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60 } else {
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61 level = as.numeric(level)
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62 }
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63 #genes = as.vector(file[,ncol])
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64
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65 # Extract Gene Entrez ID
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66 if (id_type == "Entrez") {
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67 id = select(package, ids, "ENTREZID", multiVals = "first")
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68 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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69 } else {
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70 genes_ids = c()
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71 id = select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first")
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72 if (duplicate == "TRUE") {
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73 id = unique(id)
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74 }
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75 print(id[[1]])
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76 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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77 # IDs that have NA ENTREZID
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78 NAs = id$UNIPROT[which(is.na(id$ENTREZID))]
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79 #print("IDs unable to convert to ENTREZID: ")
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80 #print(NAs)
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81 }
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82
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83 # Create basic profiles
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84 profile.CC = basicProfile(genes_ids, onto='CC', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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85 profile.BP = basicProfile(genes_ids, onto='BP', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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86 profile.MF = basicProfile(genes_ids, onto='MF', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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87 profile.ALL = basicProfile(genes_ids, onto='ANY', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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88
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89 # Print profile
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90 # printProfiles(profile)
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91
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92 return(c(profile.CC, profile.MF, profile.BP, profile.ALL))
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93 }
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94
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95 make_plot <- function(profile,percent,title,onto,plot_opt){
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96
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97 if (plot_opt == "PDF") {
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98 file_name=paste("profile_",onto,".pdf",collapse="",sep="")
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99 pdf(file_name)
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100 } else if (plot_opt == "JPEG"){
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101 file_name=paste("profile_",onto,".jpeg",collapse="",sep="")
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102 jpeg(file_name)
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103 } else if (plot_opt == "PNG"){
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104 file_name=paste("profile_",onto,".png",collapse="",sep="")
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105 png(file_name)
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106 }
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107 plotProfiles(profile, percentage=percent, multiplePlots=FALSE, aTitle=title)
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108 dev.off()
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109 }
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110
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111 goprofiles = function() {
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112 args <- commandArgs(TRUE)
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113 if(length(args)<1) {
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114 args <- c("--help")
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115 }
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116
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117 # Help section
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118 if("--help" %in% args) {
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119 cat("Selection and Annotation HPA
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120 Arguments:
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121 --input_type: type of input (list of id or filename)
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122 --input: input
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123 --ncol: the column number which you would like to apply...
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124 --header: true/false if your file contains a header
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125 --id_type: the type of input IDs (UniProt/EntrezID)
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126 --onto_opt: ontology options
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127 --plot_opt: plot extension options (PDF/JPEG/PNG)
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128 --level: 1-3
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129 --per
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130 --title: title of the plot
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131 --duplicate: remove dupliate input IDs (true/false)
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132 --text_output: text output filename \n
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133 --species")
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134 q(save="no")
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135 }
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136
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137 # Parse arguments
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138 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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139 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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140 args <- as.list(as.character(argsDF$V2))
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141 names(args) <- argsDF$V1
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142
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143 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")
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144 #load("/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")
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145
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146 id_type = args$id_type
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147 input_type = args$input_type
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148 if (input_type == "text") {
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149 input = strsplit(args$input, "[ \t\n]+")[[1]]
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150 } else if (input_type == "file") {
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151 filename = args$input
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152 ncol = args$ncol
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153 # Check ncol
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154 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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155 stop("Please enter an integer for level")
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156 } else {
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157 ncol = as.numeric(gsub("c", "", ncol))
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158 }
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159 header = str2bool(args$header)
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160 # Get file content
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161 file = read_file(filename, header)
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162 # Extract Protein IDs list
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163 input = unlist(strsplit(as.character(file[,ncol]),";"))
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164 input = input [which(!is.na(input))]
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165 }
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166
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167 if (! any(check_ids(input,id_type))){
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168 stop(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file"))
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169 }
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170
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171 ontoopt = strsplit(args$onto_opt, ",")[[1]]
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172 onto_pos = as.integer(gsub("BP",3,gsub("MF",2,gsub("CC",1,ontoopt))))
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173 plotopt = args$plot_opt
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174 level = args$level
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175 per = as.logical(args$per)
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176 title = args$title
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177 duplicate = args$duplicate
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178 text_output = args$text_output
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179 species=args$species
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180
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181 profiles = getprofile(input, id_type, level, duplicate,species)
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182
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183 for (index in onto_pos) {
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184 onto = names(profiles[index])
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185 profile=profiles[index]
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186 make_plot(profile,per,title,onto,plotopt)
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187 text_output=paste("goProfiles_",onto,"_",title,".tsv",sep="",collapse="")
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188 profile = as.data.frame(profile)
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189 profile <- as.data.frame(apply(profile, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" and " " to NA
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190 write.table(profile, text_output, sep="\t", row.names = FALSE, quote=FALSE, col.names = T)
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191 }
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192 }
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193
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194 goprofiles()