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45
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1 #msg.file<-file("RnBeads.messages.out", open="w")
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2 #sink(file=msg.file)
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3
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4
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5 ## add the RnBeads dependencies if we are on a cloud share-instance
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6 if("Rsitelibrary" %in% list.files("/mnt")){
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7 .libPaths("/mnt/galaxy/Rsitelibrary")
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8 }
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9
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10 if(!'wordcloud' %in% rownames(installed.packages())){
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11 install.packages('wordcloud',repos='http://cran.us.r-project.org')
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12 }
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13
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14 suppressWarnings(suppressPackageStartupMessages(library(RnBeads)))
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15 suppressWarnings(suppressPackageStartupMessages(library(getopt)))
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16
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17
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18 fname <- system.file(file.path("extdata", "options.txt"), package = "RnBeads")
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19 table.options <- read.delim(fname, quote = "", stringsAsFactors = FALSE)
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20 rownames(table.options) <- table.options[, "Name"]
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21
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22 all.opts<-table.options$Name
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23 #all.opts<-names(rnb.options())
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24 #opt.class<-RnBeads:::OPTION.TYPES[-28]
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25 opt.class<-table.options$Type
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26 names(opt.class)<-all.opts
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27 #all.opts<-names(opt.class)
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28 #all.opts<-paste("--", all.opts, sep="")
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29 #all.opts<-gsub("\\.([a-z])", "\\U\\1", all.opts, perl=TRUE)
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30 all.opts<-gsub("\\.","-", all.opts)
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31 #opt.class<-sapply(rnb.options(), class)
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32
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33 rnb.opt.spec<-data.frame(
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34 Long=all.opts,
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35 Short=as.character(1:length(all.opts)),
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36 Mask=c(1,2)[as.integer((opt.class=="logical"))+1],
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37 Type=opt.class)
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38
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39 ### automated xml file preparation
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40 #xml.strings<-apply(rnb.opt.spec,1, function(row){
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41 #
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42 # opt.lab<-gsub("-", ".", row[1])
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43 # opt.def.val<-rnb.getOption(opt.lab)
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44 # #print(opt.def.val)
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45 # opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
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46 # tf.opt<-"\t\t\t<option value=\"True\">True</option>\n\t\t\t<option value=\"False\">False</option>"
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47 # opt.lab<-paste(opt.lab, gsub("\\."," ", row[4]), sep=", ")
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48 # if(row[4]=="logical"){
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49 # opt.type<-'select'
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50 # if(!is.null(opt.def.val) && opt.def.val)
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51 # opt.def.val<-"1" else
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52 # opt.def.val<-"0"
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53 # string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\">\n%s\n\t\t</param>\n", opt.name, opt.type, opt.lab, opt.def.val, tf.opt)
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54 # }else{
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55 # opt.type<-'text'
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56 # if(length(opt.def.val)<1L){
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57 # opt.def.val<-""
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58 # }else{
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59 # if(!is.null(opt.def.val) && opt.def.val!="")
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60 # opt.def.val<-paste(opt.def.val, collapse=",") else
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61 # opt.def.val<-""
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62 # }
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63 # string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\"/>\n", opt.name, opt.type, opt.lab, opt.def.val)
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64 # }
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65 # string
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66 # })
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67 ##cat(xml.strings, sep="", file="automated.settings.xml.txt")
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68 #
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69 #opt.def.strings<-apply(rnb.opt.spec,1, function(row){
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70 #
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71 # opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
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72 # opt.long<-row[1]
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73 # opt.short<-row[2]
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74 #
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75 # if(row[4]=="logical"){
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76 # def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long)
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77 # }else{
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78 # def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s=\"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name)
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79 # }
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80 # def.string
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81 #
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82 # })
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83 #cat(opt.def.strings, sep="", file="automated.option.assignments.txt")
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84
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85
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86 rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type)
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87 rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type)
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88 rnb.opt.spec<-rbind(data.frame(
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89 Long=c("data-type", "pheno", "idat-dir","idat-files","bed-files", "gs-report", "geo-series", "betas", "pvals","output-file", "report-dir"),
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90 Short=c("d","s","a","i","f","g","e","b","p","r","o"),
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91 Mask=c(1,2,2,2,2,2,2,2,2,1,1),
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92 Type=c("character","character","character","character","character","character","character","character","character","character", "character")),
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93 rnb.opt.spec)
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94
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95 opts<-getopt(as.matrix(rnb.opt.spec))
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96 #opts<-getopt(as.matrix(rnb.opt.spec), opt=list("--data-type=idats","--report-dir=dir", "--idats=file1\tfile2"))
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97 print(opts)
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98
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99 if(opts[["data-type"]]=="idatDir"){
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100
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101 data.source<-list()
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102 data.type<-"idat.dir"
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103 data.source[["idat.dir"]]<-opts[["idat-dir"]]
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104 data.source[["sample.sheet"]]<-opts[["pheno"]]
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105
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106 }else if(opts[["data-type"]]=="idatFiles"){
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107
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108 data.type<-"idat.dir"
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109 file.string<-gsub(" ","", opts[["idat-files"]])
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110 files<-strsplit(file.string, ",")[[1]]
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111 files<-files[files!=""]
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112 bed.dir<-sprintf("%s_beds",opts[["report-dir"]])
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113 dir.create(bed.dir)
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114 file.copy(files, bed.dir)
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115 for(dat.file in list.files(bed.dir, full.names = TRUE)){
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116 file.rename(dat.file, gsub("\\.dat", ".bed", dat.file))
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117 }
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118 data.source<-list()
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119 data.source[["bed.dir"]]<-bed.dir
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120 data.source[["sample.sheet"]]<-opts[["pheno"]]
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121
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122
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123 }else if(opts[["data-type"]]=="GS.report"){
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124
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125 data.type<-"GS.report"
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126 data.source<-opts[["gs-report"]]
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127
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128 }else if(opts[["data-type"]]=="GEO"){
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129
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130 data.type<-"GEO"
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131 data.source<-opts[["geo-series"]]
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132
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133 }else if(opts[["data-type"]]=="data.files"){
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134
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135 data.type<-"GEO"
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136 data.source<-opts[["geo-series"]]
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137
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138 }else if(opts[["data-type"]]=="data.files"){
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139
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140 data.type<-"data.files"
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141 data.source<-c(opts[["pheno"]], opts[["betas"]])
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142 if(!is.null(opts[["pvals"]]))
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143 data.source<-c(data.source, opts[["pvals"]])
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144
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145 }else if(opts[["data-type"]]=="bed.dir"){
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146
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147 data.type<-"bed.dir"
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148 file.string<-gsub(" ","", opts[["bed-files"]])
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149 files<-strsplit(file.string, ",")[[1]]
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150 files<-files[files!=""]
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151 bed.dir<-sprintf("%s_beds",opts[["report-dir"]])
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152 dir.create(bed.dir)
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153 file.copy(files, bed.dir)
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154 for(dat.file in list.files(bed.dir, full.names = TRUE)){
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155 file.rename(dat.file, gsub("\\.dat", ".bed", dat.file))
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156 }
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157 data.source<-list()
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158 data.source[["bed.dir"]]<-bed.dir
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159
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160 logger.start(fname="NA")
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161 sample.sheet<-read.sample.annotation(opts[["pheno"]])
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162 logger.close()
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163 if(length(files) < nrow(sample.sheet))
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164 stop("Not all bed files are present")
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165
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166 cn<-colnames(sample.sheet)
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167 dat.files<-sapply(strsplit(files, "\\/"), function(el) el[length(el)])
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168 sample.sheet<-cbind(sample.sheet, gsub("\\.dat", ".bed", dat.files))
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169 colnames(sample.sheet)<-c(cn, "BED_files")
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170 data.source[["sample.sheet"]]<-sample.sheet
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171 }
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172
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173 if("logging" %in% names(opts)){ # TODO create a cleaner way of checking whether the full options set was supplied
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174
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175 dump<-sapply(names(opt.class), function(on){
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176 getoptname<-gsub("-", "\\.","-",on)
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177 if(getoptname %in% names(opts)){
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178 if(opt.class[on]=="logical"){
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179 ov<-TRUE
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180 }else if(opt.class %in% c("character","character.vector")){
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181 ov<-opts[[getoptname]]
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182 ov<-gsub("\"", "", ov)
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183 if(opt.class=="character.vector"){
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184 ov<-as.character(strsplit(ov,","))
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185 }
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186
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187 }else if(opt.class %in% c("integer","numeric","integer.vector","numeric.vector")){
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188 ov<-opts[[getoptname]]
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189 ov<-gsub("\"", "", ov)
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190 if(opt.class %in% c("integer.vector","numeric.vector")){
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191 ov<-as.character(strsplit(ov,","))
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192 }
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193 }
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194 eval(parse(text=sprintf("rnb.options(%s=ov)",on)))
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195 }
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196 })
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197
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198 logical.opts<-names(opt.class[opt.class=="logical"])
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199 logical.opts.false<-logical.opts[!logical.opts %in% gsub("-",".",names(opts))]
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200
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201
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202 dump<-sapply(logical.opts.false, function(on){
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203 eval(parse(text=sprintf("rnb.options(%s=FALSE)",on)))
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204 })
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205 }
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206
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207 print(rnb.options())
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208
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209 #report.out.dir<-sprintf("%s_rnbReport", tempdir())
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210 report.out.dir<-opts[["report-dir"]]
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211 print("Starting RnBeads with the following inputs:")
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212 print(data.source)
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213 print(report.out.dir)
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214 print(data.type)
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215 rnb.run.analysis(data.source=data.source, dir.report=report.out.dir, data.type=data.type)
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216
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217
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218 #sink(file=NULL)
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219 #flush(msg.file)
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220 #close(msg.file) |
