Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.R @ 7:3e138d54c105 draft

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planemo upload commit 4e898239997b7ef266b1d0ce0a4c7cdec31b4ecd-dirty
author proteore
date Fri, 21 Sep 2018 10:08:02 -0400
parents 6afe8166a9a4
children 386145573c19
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1 options(warn=-1) #TURN OFF WARNINGS !!!!!!
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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 readfile = function(filename, header) {
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8 if (header == "true") {
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9 # Read only first line of the file as header:
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10 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
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11 #Read the data of the files (skipping the first row)
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12 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
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13 # Remove empty rows
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14 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
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15 #And assign the header to the data
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16 names(file) <- headers
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17 }
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18 else {
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19 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
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20 # Remove empty rows
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21 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
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22 }
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23 return(file)
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24 }
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26 check_ids <- function(vector,type) {
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27 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})$"
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28 entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
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29 if (type == "Entrez"){
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30 return(grepl(entrez_id,vector))
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31 } else if (type == "UniProt") {
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32 return(grepl(uniprot_pattern,vector))
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33 }
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34 }
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35
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36 getprofile = function(ids, id_type, level, duplicate,species) {
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37 ####################################################################
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38 # Arguments
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39 # - ids: list of input IDs
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40 # - id_type: type of input IDs (UniProt/ENTREZID)
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41 # - level
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42 # - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE)
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43 # - species
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44 ####################################################################
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45
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46 library(species, character.only = TRUE, quietly = TRUE)
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47
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48 if (species=="org.Hs.eg.db"){
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49 package=org.Hs.eg.db
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50 } else if (species=="org.Mm.eg.db"){
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51 package=org.Mm.eg.db
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52 }
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55
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56 # Check if level is number
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57 if (! as.numeric(level) %% 1 == 0) {
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58 stop("Please enter an integer for level")
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59 } else {
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60 level = as.numeric(level)
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61 }
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62 #genes = as.vector(file[,ncol])
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63
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64 # Extract Gene Entrez ID
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65 if (id_type == "Entrez") {
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66 id = select(package, ids, "ENTREZID", multiVals = "first")
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67 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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68 } else {
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69 genes_ids = c()
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70 id = select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first")
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71 if (duplicate == "TRUE") {
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72 id = unique(id)
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73 }
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74 print(id[[1]])
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75 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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76 # IDs that have NA ENTREZID
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77 NAs = id$UNIPROT[which(is.na(id$ENTREZID))]
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78 print("IDs unable to convert to ENTREZID: ")
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79 print(NAs)
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80 }
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81
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82 # Create basic profiles
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83 profile.CC = basicProfile(genes_ids, onto='CC', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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84 profile.BP = basicProfile(genes_ids, onto='BP', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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85 profile.MF = basicProfile(genes_ids, onto='MF', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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86 profile.ALL = basicProfile(genes_ids, onto='ANY', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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87
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88 # Print profile
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89 # printProfiles(profile)
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90
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91 return(c(profile.CC, profile.MF, profile.BP, profile.ALL))
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92 }
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93
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94 # Plot profiles to PNG
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95 plotPNG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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96 if (!is.null(profile.CC)) {
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97 png("profile.CC.png")
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98 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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99 dev.off()
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100 }
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101 if (!is.null(profile.BP)) {
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102 png("profile.BP.png")
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103 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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104 dev.off()
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105 }
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106 if (!is.null(profile.MF)) {
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107 png("profile.MF.png")
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108 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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109 dev.off()
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110 }
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111 if (!is.null(profile.ALL)) {
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112 png("profile.ALL.png")
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113 plotProfiles(profile.ALL, percentage=per, multiplePlots=T, aTitle=title)
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114 dev.off()
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115 }
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116 }
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117
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118 # Plot profiles to JPEG
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119 plotJPEG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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120 if (!is.null(profile.CC)) {
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121 jpeg("profile.CC.jpeg")
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122 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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123 dev.off()
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124 }
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125 if (!is.null(profile.BP)) {
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126 jpeg("profile.BP.jpeg")
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127 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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128 dev.off()
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129 }
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130 if (!is.null(profile.MF)) {
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131 jpeg("profile.MF.jpeg")
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132 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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133 dev.off()
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134 }
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135 if (!is.null(profile.ALL)) {
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136 jpeg("profile.ALL.jpeg")
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137 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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138 dev.off()
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139 }
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140 }
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141
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142 # Plot profiles to PDF
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143 plotPDF = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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144 if (!is.null(profile.CC)) {
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145 pdf("profile.CC.pdf")
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146 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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147 dev.off()
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148 }
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149 if (!is.null(profile.BP)) {
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150 pdf("profile.BP.pdf")
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151 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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152 dev.off()
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153 }
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154 if (!is.null(profile.MF)) {
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155 pdf("profile.MF.pdf")
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156 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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157 dev.off()
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158 }
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159 if (!is.null(profile.ALL)) {
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160 #print("all")
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161 pdf("profile.ALL.pdf")
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162 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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163 dev.off()
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164 }
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165 }
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166
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167 goprofiles = function() {
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168 args <- commandArgs(TRUE)
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169 if(length(args)<1) {
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170 args <- c("--help")
0
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171 }
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172
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173 # Help section
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174 if("--help" %in% args) {
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175 cat("Selection and Annotation HPA
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176 Arguments:
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177 --input_type: type of input (list of id or filename)
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178 --input: input
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179 --ncol: the column number which you would like to apply...
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180 --header: true/false if your file contains a header
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181 --id_type: the type of input IDs (UniProt/EntrezID)
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182 --onto_opt: ontology options
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183 --plot_opt: plot extension options (PDF/JPEG/PNG)
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184 --level: 1-3
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185 --per
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186 --title: title of the plot
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187 --duplicate: remove dupliate input IDs (true/false)
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188 --text_output: text output filename \n
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189 --species")
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190 q(save="no")
0
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191 }
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192
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193 # Parse arguments
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194 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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195 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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196 args <- as.list(as.character(argsDF$V2))
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197 names(args) <- argsDF$V1
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198
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199 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")
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200 #load("/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")
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201
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202 id_type = args$id_type
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203 input_type = args$input_type
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204 if (input_type == "text") {
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205 input = strsplit(args$input, "[ \t\n]+")[[1]]
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206 } else if (input_type == "file") {
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207 filename = args$input
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208 ncol = args$ncol
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209 # Check ncol
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210 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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211 stop("Please enter an integer for level")
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212 } else {
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213 ncol = as.numeric(gsub("c", "", ncol))
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214 }
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215 header = args$header
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216 # Get file content
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217 file = readfile(filename, header)
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218 # Extract Protein IDs list
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219 input = unlist(strsplit(as.character(file[,ncol]),";"))
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220 input = input [which(!is.na(input))]
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221 }
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222
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223 if (! any(check_ids(input,id_type))){
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224 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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225 }
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226
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227 ontoopt = strsplit(args$onto_opt, ",")[[1]]
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228 #print(ontoopt)
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229 #plotopt = strsplit(args[3], ",")
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230 plotopt = args$plot_opt
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231 level = args$level
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232 per = as.logical(args$per)
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233 title = args$title
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234 duplicate = args$duplicate
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235 text_output = args$text_output
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236 species=args$species
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237
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238 profiles = getprofile(input, id_type, level, duplicate,species)
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239 profile.CC = profiles[1]
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240 #print(profile.CC)
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241 profile.MF = profiles[2]
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242 #print(profile.MF)
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243 profile.BP = profiles[3]
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244 #print(profile.BP)
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245 profile.ALL = profiles[-3:-1]
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246 #print(profile.ALL)
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247 #c(profile.ALL, profile.CC, profile.MF, profile.BP)
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248
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249 if ("CC" %in% ontoopt) {
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250 write.table(profile.CC, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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251 if (grepl("PNG", plotopt)) {
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252 plotPNG(profile.CC=profile.CC, per=per, title=title)
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253 }
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254 if (grepl("JPEG", plotopt)) {
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255 plotJPEG(profile.CC = profile.CC, per=per, title=title)
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256 }
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257 if (grepl("PDF", plotopt)) {
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258 plotPDF(profile.CC = profile.CC, per=per, title=title)
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259 }
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260 }
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261 if ("MF" %in% ontoopt) {
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262 write.table(profile.MF, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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263 if (grepl("PNG", plotopt)) {
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264 plotPNG(profile.MF = profile.MF, per=per, title=title)
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265 }
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266 if (grepl("JPEG", plotopt)) {
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267 plotJPEG(profile.MF = profile.MF, per=per, title=title)
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268 }
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269 if (grepl("PDF", plotopt)) {
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270 plotPDF(profile.MF = profile.MF, per=per, title=title)
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271 }
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272 }
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273 if ("BP" %in% ontoopt) {
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274 write.table(profile.BP, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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275 if (grepl("PNG", plotopt)) {
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276 plotPNG(profile.BP = profile.BP, per=per, title=title)
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277 }
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278 if (grepl("JPEG", plotopt)) {
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279 plotJPEG(profile.BP = profile.BP, per=per, title=title)
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280 }
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281 if (grepl("PDF", plotopt)) {
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282 plotPDF(profile.BP = profile.BP, per=per, title=title)
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283 }
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284 }
0
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285 }
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286
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287 goprofiles()