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1 #!/usr/bin/Rscript
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2
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3 #' Returns file name of calling Rscript
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4 #'
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5 #' \code{get_Rscript_filename} returns the file name of calling Rscript
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6 #' @return A string with the filename of the calling script.
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7 #' If not found (i.e. you are in a interactive session) returns NA.
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8 #'
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9 #' @export
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10 get_Rscript_filename <- function() {
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11 prog <- sub("--file=", "", grep("--file=", commandArgs(), value=TRUE)[1])
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12 if( .Platform$OS.type == "windows") {
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13 prog <- gsub("\\\\", "\\\\\\\\", prog)
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14 }
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15 prog
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16 }
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17
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18 #' Recursively sorts a list
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19 #'
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20 #' \code{sort_list} returns a sorted list
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21 #' @param unsorted_list A list.
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22 #' @return A sorted list.
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23 #' @export
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24 sort_list <- function(unsorted_list) {
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25 for(ii in seq(along=unsorted_list)) {
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26 if(is.list(unsorted_list[[ii]])) {
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27 unsorted_list[[ii]] <- sort_list(unsorted_list[[ii]])
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28 }
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29 }
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30 unsorted_list[sort(names(unsorted_list))]
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31 }
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32
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33 #' #!/path/to/Rscript
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34 #' library('getopt');
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35 #' #get options, using the spec as defined by the enclosed list.
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36 #' #we read the options from the default: commandArgs(TRUE).
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37 #' spec = matrix(c(
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38 #' 'verbose', 'v', 2, "integer",
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39 #' 'help' , 'h', 0, "logical",
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40 #' 'count' , 'c', 1, "integer",
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41 #' 'mean' , 'm', 1, "double",
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42 #' 'sd' , 's', 1, "double"
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43 #' ), byrow=TRUE, ncol=4);
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44 #' opt = getopt(spec);
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45 #'
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46 #' # if help was asked for print a friendly message
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47 #' # and exit with a non-zero error code
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48 #' if ( !is.null(opt$help) ) {
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49 #' cat(getopt(spec, usage=TRUE));
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50 #' q(status=1);
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51 #' }
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52 #'
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53 #' #set some reasonable defaults for the options that are needed,
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54 #' #but were not specified.
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55 #' if ( is.null(opt$mean ) ) { opt$mean = 0 }
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56 #' if ( is.null(opt$sd ) ) { opt$sd = 1 }
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57 #' if ( is.null(opt$count ) ) { opt$count = 10 }
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58 #' if ( is.null(opt$verbose ) ) { opt$verbose = FALSE }
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59 #'
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60 #' #print some progress messages to stderr, if requested.
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61 #' if ( opt$verbose ) { write("writing...",stderr()); }
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62 #'
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63 #' #do some operation based on user input.
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64 #' cat(paste(rnorm(opt$count,mean=opt$mean,sd=opt$sd),collapse="\n"));
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65 #' cat("\n");
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66 #'
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67 #' #signal success and exit.
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68 #' #q(status=0);
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69 getopt = function (spec=NULL,opt=commandArgs(TRUE),command=get_Rscript_filename(),usage=FALSE,debug=FALSE) {
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70
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71 # littler compatibility - map argv vector to opt
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72 if (exists("argv", where = .GlobalEnv, inherits = FALSE)) {
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73 opt = get("argv", envir = .GlobalEnv);
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74 }
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75
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76 ncol=4;
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77 maxcol=6;
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78 col.long.name = 1;
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79 col.short.name = 2;
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80 col.has.argument = 3;
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81 col.mode = 4;
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82 col.description = 5;
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83
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84 flag.no.argument = 0;
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85 flag.required.argument = 1;
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86 flag.optional.argument = 2;
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87
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88 result = list();
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89 result$ARGS = vector(mode="character");
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90
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91 #no spec. fail.
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92 if ( is.null(spec) ) {
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93 stop('argument "spec" must be non-null.');
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94
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95 #spec is not a matrix. attempt to coerce, if possible. issue a warning.
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96 } else if ( !is.matrix(spec) ) {
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97 if ( length(spec)/4 == as.integer(length(spec)/4) ) {
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98 warning('argument "spec" was coerced to a 4-column (row-major) matrix. use a matrix to prevent the coercion');
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99 spec = matrix( spec, ncol=ncol, byrow=TRUE );
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100 } else {
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101 stop('argument "spec" must be a matrix, or a character vector with length divisible by 4, rtfm.');
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102 }
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103
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104 #spec is a matrix, but it has too few columns.
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105 } else if ( dim(spec)[2] < ncol ) {
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106 stop(paste('"spec" should have at least ",ncol," columns.',sep=''));
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107
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108 #spec is a matrix, but it has too many columns.
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109 } else if ( dim(spec)[2] > maxcol ) {
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110 stop(paste('"spec" should have no more than ",maxcol," columns.',sep=''));
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111
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112 #spec is a matrix, and it has some optional columns.
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113 } else if ( dim(spec)[2] != ncol ) {
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114 ncol = dim(spec)[2];
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115 }
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116
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117 #sanity check. make sure long names are unique, and short names are unique.
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118 if ( length(unique(spec[,col.long.name])) != length(spec[,col.long.name]) ) {
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119 stop(paste('redundant long names for flags (column ',col.long.name,').',sep=''));
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120 }
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121 if ( length(na.omit(unique(spec[,col.short.name]))) != length(na.omit(spec[,col.short.name])) ) {
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122 stop(paste('redundant short names for flags (column ',col.short.name,').',sep=''));
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123 }
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124 # convert numeric type to double type
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125 spec[,4] <- gsub("numeric", "double", spec[,4])
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126
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127 # if usage=TRUE, don't process opt, but generate a usage string from the data in spec
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128 if ( usage ) {
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129 ret = '';
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130 ret = paste(ret,"Usage: ",command,sep='');
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131 for ( j in 1:(dim(spec))[1] ) {
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132 ret = paste(ret,' [-[-',spec[j,col.long.name],'|',spec[j,col.short.name],']',sep='');
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133 if (spec[j,col.has.argument] == flag.no.argument) {
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134 ret = paste(ret,']',sep='');
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135 } else if (spec[j,col.has.argument] == flag.required.argument) {
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136 ret = paste(ret,' <',spec[j,col.mode],'>]',sep='');
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137 } else if (spec[j,col.has.argument] == flag.optional.argument) {
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138 ret = paste(ret,' [<',spec[j,col.mode],'>]]',sep='');
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139 }
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140 }
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141 # include usage strings
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142 if ( ncol >= 5 ) {
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143 max.long = max(apply(cbind(spec[,col.long.name]),1,function(x)length(strsplit(x,'')[[1]])));
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144 ret = paste(ret,"\n",sep='');
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145 for (j in 1:(dim(spec))[1] ) {
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146 ret = paste(ret,sprintf(paste(" -%s|--%-",max.long,"s %s\n",sep=''),
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147 spec[j,col.short.name],spec[j,col.long.name],spec[j,col.description]
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148 ),sep='');
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149 }
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150 }
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151 else {
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152 ret = paste(ret,"\n",sep='');
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153 }
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154 return(ret);
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155 }
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156
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157 #XXX check spec validity here. e.g. column three should be convertible to integer
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158
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159 i = 1;
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160
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161 while ( i <= length(opt) ) {
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162 if ( debug ) print(paste("processing",opt[i]));
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163
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164 current.flag = 0; #XXX use NA
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165 optstring = opt[i];
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166
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167
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168 #long flag
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169 if ( substr(optstring, 1, 2) == '--' ) {
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170 if ( debug ) print(paste(" long option:",opt[i]));
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171
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172 optstring = substring(optstring,3);
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173
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174 this.flag = NA;
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175 this.argument = NA;
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176 kv = strsplit(optstring, '=')[[1]];
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177 if ( !is.na(kv[2]) ) {
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178 this.flag = kv[1];
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179 this.argument = paste(kv[-1], collapse="=");
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180 } else {
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181 this.flag = optstring;
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182 }
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183
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184 rowmatch = grep( this.flag, spec[,col.long.name],fixed=TRUE );
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185
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186 #long flag is invalid, matches no options
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187 if ( length(rowmatch) == 0 ) {
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188 stop(paste('long flag "', this.flag, '" is invalid', sep=''));
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189
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190 #long flag is ambiguous, matches too many options
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191 } else if ( length(rowmatch) > 1 ) {
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192 # check if there is an exact match and use that
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193 rowmatch = which(this.flag == spec[,col.long.name])
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194 if(length(rowmatch) == 0) {
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195 stop(paste('long flag "', this.flag, '" is ambiguous', sep=''));
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196 }
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197 }
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198
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199 #if we have an argument
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200 if ( !is.na(this.argument) ) {
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201 #if we can't accept the argument, bail out
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202 if ( spec[rowmatch, col.has.argument] == flag.no.argument ) {
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203 stop(paste('long flag "', this.flag, '" accepts no arguments', sep=''));
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204
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205 #otherwise assign the argument to the flag
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206 } else {
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207 storage.mode(this.argument) = spec[rowmatch, col.mode];
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208 result[spec[rowmatch, col.long.name]] = this.argument;
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209 i = i + 1;
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210 next;
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211 }
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212
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213 #otherwise, we don't have an argument
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214 } else {
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215 #if we require an argument, bail out
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216 ###if ( spec[rowmatch, col.has.argument] == flag.required.argument ) {
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217 ### stop(paste('long flag "', this.flag, '" requires an argument', sep=''));
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218
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219 #long flag has no attached argument. set flag as present. set current.flag so we can peek ahead later and consume the argument if it's there
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220 ###} else {
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221 result[spec[rowmatch, col.long.name]] = TRUE;
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222 current.flag = rowmatch;
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223 ###}
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224 }
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225
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226 #short flag(s)
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227 } else if ( substr(optstring, 1, 1) == '-' ) {
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228 if ( debug ) print(paste(" short option:",opt[i]));
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229
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230 these.flags = strsplit(optstring,'')[[1]];
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231
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232 done = FALSE;
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233 for ( j in 2:length(these.flags) ) {
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234 this.flag = these.flags[j];
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235 rowmatch = grep( this.flag, spec[,col.short.name],fixed=TRUE );
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236
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237 #short flag is invalid, matches no options
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238 if ( length(rowmatch) == 0 ) {
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239 stop(paste('short flag "', this.flag, '" is invalid', sep=''));
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240
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241 #short flag is ambiguous, matches too many options
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242 } else if ( length(rowmatch) > 1 ) {
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243 stop(paste('short flag "', this.flag, '" is ambiguous', sep=''));
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244
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245 #short flag has an argument, but is not the last in a compound flag string
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246 } else if ( j < length(these.flags) & spec[rowmatch,col.has.argument] == flag.required.argument ) {
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247 stop(paste('short flag "', this.flag, '" requires an argument, but has none', sep=''));
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248
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249 #short flag has no argument, flag it as present
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250 } else if ( spec[rowmatch,col.has.argument] == flag.no.argument ) {
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251 result[spec[rowmatch, col.long.name]] = TRUE;
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252 done = TRUE;
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253
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254 #can't definitively process this flag yet, need to see if next option is an argument or not
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255 } else {
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256 result[spec[rowmatch, col.long.name]] = TRUE;
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257 current.flag = rowmatch;
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258 done = FALSE;
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259 }
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260 }
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261 if ( done ) {
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262 i = i + 1;
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263 next;
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264 }
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265 }
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266
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267 #invalid opt
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268 if ( current.flag == 0 ) {
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269 stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep=''));
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270 #TBD support for positional args
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271 #if ( debug ) print(paste('"', optstring, '" not a valid option. It is appended to getopt(...)$ARGS', sep=''));
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272 #result$ARGS = append(result$ARGS, optstring);
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273
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274 # some dangling flag, handle it
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275 } else if ( current.flag > 0 ) {
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276 if ( debug ) print(' dangling flag');
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277 if ( length(opt) > i ) {
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278 peek.optstring = opt[i + 1];
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279 if ( debug ) print(paste(' peeking ahead at: "',peek.optstring,'"',sep=''));
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280
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281 #got an argument. attach it, increment the index, and move on to the next option. we don't allow arguments beginning with '-' UNLESS
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282 #specfile indicates the value is an "integer" or "double", in which case we allow a leading dash (and verify trailing digits/decimals).
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283 if ( substr(peek.optstring, 1, 1) != '-' |
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284 #match negative double
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285 ( substr(peek.optstring, 1, 1) == '-'
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286 & regexpr('^-[0123456789]*\\.?[0123456789]+$',peek.optstring) > 0
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287 & spec[current.flag, col.mode]== 'double'
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288 ) |
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289 #match negative integer
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290 ( substr(peek.optstring, 1, 1) == '-'
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291 & regexpr('^-[0123456789]+$',peek.optstring) > 0
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292 & spec[current.flag, col.mode]== 'integer'
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293 )
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294 ) {
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295 if ( debug ) print(paste(' consuming argument *',peek.optstring,'*',sep=''));
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296
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297 storage.mode(peek.optstring) = spec[current.flag, col.mode];
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298 result[spec[current.flag, col.long.name]] = peek.optstring;
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299 i = i + 1;
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300
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301 #a lone dash
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302 } else if ( substr(peek.optstring, 1, 1) == '-' & length(strsplit(peek.optstring,'')[[1]]) == 1 ) {
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303 if ( debug ) print(' consuming "lone dash" argument');
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304 storage.mode(peek.optstring) = spec[current.flag, col.mode];
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305 result[spec[current.flag, col.long.name]] = peek.optstring;
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306 i = i + 1;
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307
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308 #no argument
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309 } else {
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310 if ( debug ) print(' no argument!');
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311
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312 #if we require an argument, bail out
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313 if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
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314 stop(paste('flag "', this.flag, '" requires an argument', sep=''));
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315
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316 #otherwise set flag as present.
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317 } else if (
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318 spec[current.flag, col.has.argument] == flag.optional.argument |
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319 spec[current.flag, col.has.argument] == flag.no.argument
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320 ) {
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321 x = TRUE;
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322 storage.mode(x) = spec[current.flag, col.mode];
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323 result[spec[current.flag, col.long.name]] = x;
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324 } else {
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325 stop(paste("This should never happen.",
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326 "Is your spec argument correct? Maybe you forgot to set",
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327 "ncol=4, byrow=TRUE in your matrix call?"));
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328 }
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329 }
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330 #trailing flag without required argument
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331 } else if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
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332 stop(paste('flag "', this.flag, '" requires an argument', sep=''));
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333
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334 #trailing flag without optional argument
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335 } else if ( spec[current.flag, col.has.argument] == flag.optional.argument ) {
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336 x = TRUE;
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337 storage.mode(x) = spec[current.flag, col.mode];
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338 result[spec[current.flag, col.long.name]] = x;
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339
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340 #trailing flag without argument
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341 } else if ( spec[current.flag, col.has.argument] == flag.no.argument ) {
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342 x = TRUE;
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343 storage.mode(x) = spec[current.flag, col.mode];
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344 result[spec[current.flag, col.long.name]] = x;
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345 } else {
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346 stop("this should never happen (2). please inform the author.");
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347 }
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348 #no dangling flag, nothing to do.
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349 } else {
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350 }
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351
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352 i = i+1;
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353 }
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354 return(result);
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355 }
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356
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357 # convert multi parameter string (i.e. key1: value, key2: value, ...) to object
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358 split <- function(argument){
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359 # process parameter string
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360 options <- list()
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361 list <- gsub("\\s","", argument)
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362 list <- strsplit(list, ",")
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363 if (length(list) > 0) {
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364 list <- list[[1]]
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365 for (entry in list) {
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366 pair <- strsplit(entry, ":")
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367 if (length(pair) > 0) {
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368 pair <- pair[[1]]
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369 if (length(pair) == 2) {
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370 options[[pair[1]]] <- pair[2]
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371 }
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372 }
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373 }
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374 }
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375 return(options)
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376 }
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377
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378 # get options, using the spec as defined by the enclosed list.
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379 spec = matrix(c(
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380 'workdir', 'w', 1, 'character', 'Work directory',
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381 'module', 'm', 1, 'character', 'Module name',
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382 'input', 'i', 1, 'character', 'Input tabular file',
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383 'columns', 'c', 1, 'character', 'Columns string',
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384 'settings', 's', 1, 'character', 'Settings string',
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385 'output', 'o', 1, 'character', 'Output tabular file',
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386 'help', 'h', 0, '', 'Help',
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387 'verbose', 'v', 0, '', 'Verbose'
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388 ), byrow=TRUE, ncol=5);
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389 opt = getopt(spec);
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390
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391 # show help
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392 if ( !is.null(opt$help) ||
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393 is.null(opt$module) ||
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394 is.null(opt$input) ||
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395 is.null(opt$columns) ||
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396 is.null(opt$output)) {
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397 cat(getopt(spec, usage=TRUE))
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398 q(status=1);
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399 }
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400
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401 # read columns/settings
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402 columns = split(opt$columns)
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403 settings = split(opt$settings)
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404
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405 # read table
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406 table <- read.table(opt$input)
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407
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408 # identify module file
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409 module_file = paste(opt$workdir, opt$module, '.r', sep='')
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410
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411 # source module
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412 source(module_file)
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413
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414 # run module
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415 l = wrapper (table, columns, settings)
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416
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417 # header
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418 header_title <- '# title - Chart Utilities (charts)'
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419 header_date <- paste('# date -', Sys.time(), sep=' ')
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420 header_module <- paste('# module -', opt$module, sep=' ')
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421 header_settings <- paste('# settings -', opt$settings, sep=' ')
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422 header_columns <- paste('# columns -', opt$columns, sep=' ')
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423
|
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424 # fill gaps
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425 if (length(l) > 0) {
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426 # print details
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|
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427 if (!is.null(opt$verbose)) {
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428 print ('Columns:')
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429 print (columns)
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430 print ('Settings:')
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431 print (settings)
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432 print ('Result:')
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433 print (l)
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|
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434 }
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|
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435
|
|
|
436 # create output file
|
|
|
437 output <- file(opt$output, open='wt')
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|
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438
|
|
|
439 # write header
|
|
|
440 writeLines('#', output)
|
|
|
441 writeLines(header_title, output)
|
|
|
442 writeLines(header_date, output)
|
|
|
443 writeLines(header_module, output)
|
|
|
444 writeLines(header_settings, output)
|
|
|
445 writeLines(header_columns, output)
|
|
|
446 writeLines('#', output)
|
|
|
447
|
|
|
448 # write table
|
|
|
449 write.table(l, file=output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
|
|
|
450
|
|
|
451 # close file
|
|
|
452 close(output)
|
|
|
453 } else {
|
|
|
454 print ('Columns:')
|
|
|
455 print (columns)
|
|
|
456 print ('Settings:')
|
|
|
457 print (settings)
|
|
|
458 print ('No output generated.')
|
|
|
459 } |
