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7
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1 library(RnBeads)
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2 library(getopt)
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3
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4
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5
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6 #all.opts<-names(rnb.options())
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7 opt.class<-RnBeads:::OPTION.TYPES[-28]
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8 all.opts<-names(opt.class)
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9 #all.opts<-paste("--", all.opts, sep="")
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10 #all.opts<-gsub("\\.([a-z])", "\\U\\1", all.opts, perl=TRUE)
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11 all.opts<-gsub("\\.","-", all.opts)
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12 #opt.class<-sapply(rnb.options(), class)
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13
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14 rnb.opt.spec<-data.frame(
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15 Long=all.opts,
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16 Short=as.character(1:length(all.opts)),
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17 Mask=c(1,2)[as.integer((opt.class=="logical"))+1],
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18 Type=opt.class)
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19
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20 ### automated xml file preparation
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21 #xml.strings<-apply(rnb.opt.spec,1, function(row){
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22 #
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23 # opt.lab<-gsub("-", ".", row[1])
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24 # opt.def.val<-rnb.getOption(opt.lab)
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25 # opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
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26 # tf.opt<-"\t\t\t<option value=\"True\">True</option>\n\t\t\t<option value=\"False\">False</option>"
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27 # opt.lab<-paste(opt.lab, gsub("\\."," ", row[4]), sep=", ")
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28 # if(row[4]=="logical"){
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29 # opt.type<-'select'
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30 # if(!is.null(opt.def.val) && opt.def.val)
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31 # opt.def.val<-"1" else
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32 # opt.def.val<-"0"
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33 # 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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34 # }else{
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35 # opt.type<-'text'
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36 # if(!is.null(opt.def.val) && opt.def.val!="")
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37 # opt.def.val<-paste(opt.def.val, collapse=",") else
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38 # opt.def.val<-""
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39 # 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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40 # }
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41 # string
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42 # })
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43 #
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8
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44 #cat(xml.strings, sep="", file="automated.settings.xml.txt")
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7
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45 #
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46 #opt.def.strings<-apply(rnb.opt.spec,1, function(row){
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47 #
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48 # opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
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49 # opt.long<-row[1]
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50 # opt.short<-row[2]
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51 #
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52 # if(row[4]=="logical"){
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53 # def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long)
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54 # }else{
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8
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55 # 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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7
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56 # }
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57 # def.string
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58 #
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59 # })
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8
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60 #cat(opt.def.strings, sep="", file="automated.option.assignments.txt")
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7
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61
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62
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63 rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type)
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64 rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type)
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65 rnb.opt.spec<-rbind(data.frame(
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66 Long=c("data-type", "pheno", "idat-dir","idat-files","bed-files", "gs-report", "geo-series", "betas", "pvals","report-dir"),
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67 Short=c("d","s","a","i","f","g","e","b","p","r"),
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68 Mask=c(1,2,2,2,2,2,2,2,2,1),
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69 Type=c("character","character","character","character","character","character","character","character","character","character")),
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70 rnb.opt.spec)
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71
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72 opts<-getopt(as.matrix(rnb.opt.spec))
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73 #opts<-getopt(as.matrix(rnb.opt.spec), opt=list("--data-type=idats","--report-dir=dir", "--idats=file1\tfile2"))
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74 print(opts)
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75
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76 if(opts[["data-type"]]=="idatDir"){
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77
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78 data.source<-list()
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79 data.type<-"idat.dir"
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80 data.source[["idat.dir"]]<-opts[["idat-dir"]]
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81 data.source[["sample.sheet"]]<-opts[["pheno"]]
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82
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83 }else if(opts[["data-type"]]=="idatFiles"){
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84
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85 data.type<-"idat.dir"
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86 files<-strsplit(opts[["idat-files"]], "\t")[[1]]
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87 idat.dir<-mkdir(file.path(opts[["report-dir"]], "idats"))
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88 file.copy(as.list(files), idat.dir)
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89 data.source<-list()
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90 data.source[["idat.dir"]]<-idat.dir
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91 data.source[["sample.sheet"]]<-opts[["pheno"]]
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92
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93
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94 }else if(opts[["data-type"]]=="GS.report"){
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95
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96 data.type<-"GS.report"
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97 data.source<-opts[["gs-report"]]
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98
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99 }else if(opts[["data-type"]]=="GEO"){
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100
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101 data.type<-"GEO"
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102 data.source<-opts[["geo-series"]]
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103
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104
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105 }else if(opts[["data-type"]]=="data.files"){
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106
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107 data.type<-"GEO"
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108 data.source<-opts[["geo-series"]]
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109
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110 }else if(opts[["data-type"]]=="data.files"){
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111
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112 data.type<-"data.files"
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113 data.source<-c(opts[["pheno"]], opts[["betas"]])
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114 if(!is.null(opts[["pvals"]]))
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115 data.source<-c(data.source, opts[["pvals"]])
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116
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117 }else if(opts[["data-type"]]=="beds"){
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118
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119 data.type<-"idat.dir"
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120 files<-strsplit(opts[["bed-files"]], "\t")[[1]]
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121 bed.dir<-mkdir(file.path(opts[["report-dir"]], "beds"))
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122 file.copy(as.list(files), bed.dir)
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123 data.source<-list()
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124 data.source[["bed.dir"]]<-bed.dir
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125 data.source[["sample.sheet"]]<-opts[["pheno"]]
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126
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127 }
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128
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129 dump<-sapply(names(opt.class), function(on){
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130 getoptname<-gsub("\\.","-",on)
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131 if(getoptname %in% names(opts)){
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132 if(opt.class[on]=="logical"){
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133 rnb.options(on=TRUE)
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134 }else if(opt.class %in% c("character","character.vector")){
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135 ov<-opts[[getoptname]]
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136 ov<-gsub("\"", "", ov)
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137 if(opt.class=="character.vector"){
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138 ov<-as.character(strsplit(ov,","))
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139 }
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140 rnb.options(on=ov)
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141 }else if(opt.class %in% c("integer","numeric","integer.vector","numeric.vector")){
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142 ov<-opts[[getoptname]]
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143 ov<-gsub("\"", "", ov)
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144 if(opt.class %in% c("integer.vector","numeric.vector")){
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145 ov<-as.character(strsplit(ov,","))
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146 }
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147 rnb.options(on=ov)
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148 }
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149 }
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150 })
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151
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152
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153 rnb.run.analysis(data.source=data.source, dir.report=opts[["report-dir"]], data.type=data.type)
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154
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