annotate charts.r @ 28:ece46bd32a11 draft

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author guerler
date Tue, 29 Apr 2014 15:40:21 -0400
parents b079b17dcb4a
children f294f5c9608c
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4
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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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guerler
parents:
diff changeset
203 stop(paste('long flag "', this.flag, '" accepts no arguments', sep=''));
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guerler
parents:
diff changeset
204
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guerler
parents:
diff changeset
205 #otherwise assign the argument to the flag
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guerler
parents:
diff changeset
206 } else {
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guerler
parents:
diff changeset
207 storage.mode(this.argument) = spec[rowmatch, col.mode];
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guerler
parents:
diff changeset
208 result[spec[rowmatch, col.long.name]] = this.argument;
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guerler
parents:
diff changeset
209 i = i + 1;
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guerler
parents:
diff changeset
210 next;
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guerler
parents:
diff changeset
211 }
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guerler
parents:
diff changeset
212
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guerler
parents:
diff changeset
213 #otherwise, we don't have an argument
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guerler
parents:
diff changeset
214 } else {
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guerler
parents:
diff changeset
215 #if we require an argument, bail out
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guerler
parents:
diff changeset
216 ###if ( spec[rowmatch, col.has.argument] == flag.required.argument ) {
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guerler
parents:
diff changeset
217 ### stop(paste('long flag "', this.flag, '" requires an argument', sep=''));
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guerler
parents:
diff changeset
218
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parents:
diff changeset
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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guerler
parents:
diff changeset
220 ###} else {
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parents:
diff changeset
221 result[spec[rowmatch, col.long.name]] = TRUE;
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guerler
parents:
diff changeset
222 current.flag = rowmatch;
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parents:
diff changeset
223 ###}
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guerler
parents:
diff changeset
224 }
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guerler
parents:
diff changeset
225
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parents:
diff changeset
226 #short flag(s)
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guerler
parents:
diff changeset
227 } else if ( substr(optstring, 1, 1) == '-' ) {
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guerler
parents:
diff changeset
228 if ( debug ) print(paste(" short option:",opt[i]));
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guerler
parents:
diff changeset
229
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parents:
diff changeset
230 these.flags = strsplit(optstring,'')[[1]];
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guerler
parents:
diff changeset
231
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parents:
diff changeset
232 done = FALSE;
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parents:
diff changeset
233 for ( j in 2:length(these.flags) ) {
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guerler
parents:
diff changeset
234 this.flag = these.flags[j];
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guerler
parents:
diff changeset
235 rowmatch = grep( this.flag, spec[,col.short.name],fixed=TRUE );
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guerler
parents:
diff changeset
236
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parents:
diff changeset
237 #short flag is invalid, matches no options
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guerler
parents:
diff changeset
238 if ( length(rowmatch) == 0 ) {
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guerler
parents:
diff changeset
239 stop(paste('short flag "', this.flag, '" is invalid', sep=''));
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guerler
parents:
diff changeset
240
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guerler
parents:
diff changeset
241 #short flag is ambiguous, matches too many options
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guerler
parents:
diff changeset
242 } else if ( length(rowmatch) > 1 ) {
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guerler
parents:
diff changeset
243 stop(paste('short flag "', this.flag, '" is ambiguous', sep=''));
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guerler
parents:
diff changeset
244
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parents:
diff changeset
245 #short flag has an argument, but is not the last in a compound flag string
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guerler
parents:
diff changeset
246 } else if ( j < length(these.flags) & spec[rowmatch,col.has.argument] == flag.required.argument ) {
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guerler
parents:
diff changeset
247 stop(paste('short flag "', this.flag, '" requires an argument, but has none', sep=''));
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guerler
parents:
diff changeset
248
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parents:
diff changeset
249 #short flag has no argument, flag it as present
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guerler
parents:
diff changeset
250 } else if ( spec[rowmatch,col.has.argument] == flag.no.argument ) {
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guerler
parents:
diff changeset
251 result[spec[rowmatch, col.long.name]] = TRUE;
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guerler
parents:
diff changeset
252 done = TRUE;
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parents:
diff changeset
253
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parents:
diff changeset
254 #can't definitively process this flag yet, need to see if next option is an argument or not
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guerler
parents:
diff changeset
255 } else {
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parents:
diff changeset
256 result[spec[rowmatch, col.long.name]] = TRUE;
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guerler
parents:
diff changeset
257 current.flag = rowmatch;
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guerler
parents:
diff changeset
258 done = FALSE;
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guerler
parents:
diff changeset
259 }
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guerler
parents:
diff changeset
260 }
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guerler
parents:
diff changeset
261 if ( done ) {
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guerler
parents:
diff changeset
262 i = i + 1;
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guerler
parents:
diff changeset
263 next;
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guerler
parents:
diff changeset
264 }
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guerler
parents:
diff changeset
265 }
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guerler
parents:
diff changeset
266
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parents:
diff changeset
267 #invalid opt
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parents:
diff changeset
268 if ( current.flag == 0 ) {
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parents:
diff changeset
269 stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep=''));
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parents:
diff changeset
270 #TBD support for positional args
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parents:
diff changeset
271 #if ( debug ) print(paste('"', optstring, '" not a valid option. It is appended to getopt(...)$ARGS', sep=''));
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parents:
diff changeset
272 #result$ARGS = append(result$ARGS, optstring);
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parents:
diff changeset
273
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parents:
diff changeset
274 # some dangling flag, handle it
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guerler
parents:
diff changeset
275 } else if ( current.flag > 0 ) {
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guerler
parents:
diff changeset
276 if ( debug ) print(' dangling flag');
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guerler
parents:
diff changeset
277 if ( length(opt) > i ) {
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parents:
diff changeset
278 peek.optstring = opt[i + 1];
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guerler
parents:
diff changeset
279 if ( debug ) print(paste(' peeking ahead at: "',peek.optstring,'"',sep=''));
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guerler
parents:
diff changeset
280
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parents:
diff changeset
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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guerler
parents:
diff changeset
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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guerler
parents:
diff changeset
283 if ( substr(peek.optstring, 1, 1) != '-' |
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guerler
parents:
diff changeset
284 #match negative double
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guerler
parents:
diff changeset
285 ( substr(peek.optstring, 1, 1) == '-'
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guerler
parents:
diff changeset
286 & regexpr('^-[0123456789]*\\.?[0123456789]+$',peek.optstring) > 0
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guerler
parents:
diff changeset
287 & spec[current.flag, col.mode]== 'double'
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parents:
diff changeset
288 ) |
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guerler
parents:
diff changeset
289 #match negative integer
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guerler
parents:
diff changeset
290 ( substr(peek.optstring, 1, 1) == '-'
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parents:
diff changeset
291 & regexpr('^-[0123456789]+$',peek.optstring) > 0
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guerler
parents:
diff changeset
292 & spec[current.flag, col.mode]== 'integer'
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guerler
parents:
diff changeset
293 )
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guerler
parents:
diff changeset
294 ) {
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guerler
parents:
diff changeset
295 if ( debug ) print(paste(' consuming argument *',peek.optstring,'*',sep=''));
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guerler
parents:
diff changeset
296
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parents:
diff changeset
297 storage.mode(peek.optstring) = spec[current.flag, col.mode];
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parents:
diff changeset
298 result[spec[current.flag, col.long.name]] = peek.optstring;
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guerler
parents:
diff changeset
299 i = i + 1;
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guerler
parents:
diff changeset
300
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guerler
parents:
diff changeset
301 #a lone dash
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guerler
parents:
diff changeset
302 } else if ( substr(peek.optstring, 1, 1) == '-' & length(strsplit(peek.optstring,'')[[1]]) == 1 ) {
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guerler
parents:
diff changeset
303 if ( debug ) print(' consuming "lone dash" argument');
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guerler
parents:
diff changeset
304 storage.mode(peek.optstring) = spec[current.flag, col.mode];
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guerler
parents:
diff changeset
305 result[spec[current.flag, col.long.name]] = peek.optstring;
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guerler
parents:
diff changeset
306 i = i + 1;
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guerler
parents:
diff changeset
307
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guerler
parents:
diff changeset
308 #no argument
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guerler
parents:
diff changeset
309 } else {
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guerler
parents:
diff changeset
310 if ( debug ) print(' no argument!');
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guerler
parents:
diff changeset
311
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guerler
parents:
diff changeset
312 #if we require an argument, bail out
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guerler
parents:
diff changeset
313 if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
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guerler
parents:
diff changeset
314 stop(paste('flag "', this.flag, '" requires an argument', sep=''));
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guerler
parents:
diff changeset
315
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guerler
parents:
diff changeset
316 #otherwise set flag as present.
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guerler
parents:
diff changeset
317 } else if (
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guerler
parents:
diff changeset
318 spec[current.flag, col.has.argument] == flag.optional.argument |
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guerler
parents:
diff changeset
319 spec[current.flag, col.has.argument] == flag.no.argument
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guerler
parents:
diff changeset
320 ) {
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guerler
parents:
diff changeset
321 x = TRUE;
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guerler
parents:
diff changeset
322 storage.mode(x) = spec[current.flag, col.mode];
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guerler
parents:
diff changeset
323 result[spec[current.flag, col.long.name]] = x;
b079b17dcb4a Uploaded
guerler
parents:
diff changeset
324 } else {
b079b17dcb4a Uploaded
guerler
parents:
diff changeset
325 stop(paste("This should never happen.",
b079b17dcb4a Uploaded
guerler
parents:
diff changeset
326 "Is your spec argument correct? Maybe you forgot to set",
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guerler
parents:
diff changeset
327 "ncol=4, byrow=TRUE in your matrix call?"));
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parents:
diff changeset
328 }
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guerler
parents:
diff changeset
329 }
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guerler
parents:
diff changeset
330 #trailing flag without required argument
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guerler
parents:
diff changeset
331 } else if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
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guerler
parents:
diff changeset
332 stop(paste('flag "', this.flag, '" requires an argument', sep=''));
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guerler
parents:
diff changeset
333
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guerler
parents:
diff changeset
334 #trailing flag without optional argument
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guerler
parents:
diff changeset
335 } else if ( spec[current.flag, col.has.argument] == flag.optional.argument ) {
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guerler
parents:
diff changeset
336 x = TRUE;
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parents:
diff changeset
337 storage.mode(x) = spec[current.flag, col.mode];
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guerler
parents:
diff changeset
338 result[spec[current.flag, col.long.name]] = x;
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guerler
parents:
diff changeset
339
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guerler
parents:
diff changeset
340 #trailing flag without argument
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guerler
parents:
diff changeset
341 } else if ( spec[current.flag, col.has.argument] == flag.no.argument ) {
b079b17dcb4a Uploaded
guerler
parents:
diff changeset
342 x = TRUE;
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guerler
parents:
diff changeset
343 storage.mode(x) = spec[current.flag, col.mode];
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guerler
parents:
diff changeset
344 result[spec[current.flag, col.long.name]] = x;
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guerler
parents:
diff changeset
345 } else {
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parents:
diff changeset
346 stop("this should never happen (2). please inform the author.");
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guerler
parents:
diff changeset
347 }
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guerler
parents:
diff changeset
348 #no dangling flag, nothing to do.
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guerler
parents:
diff changeset
349 } else {
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guerler
parents:
diff changeset
350 }
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guerler
parents:
diff changeset
351
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guerler
parents:
diff changeset
352 i = i+1;
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guerler
parents:
diff changeset
353 }
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guerler
parents:
diff changeset
354 return(result);
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guerler
parents:
diff changeset
355 }
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guerler
parents:
diff changeset
356
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parents:
diff changeset
357 # convert multi parameter string (i.e. key1: value, key2: value, ...) to object
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guerler
parents:
diff changeset
358 split <- function(argument){
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parents:
diff changeset
359 # process parameter string
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guerler
parents:
diff changeset
360 options <- list()
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parents:
diff changeset
361 list <- gsub("\\s","", argument)
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guerler
parents:
diff changeset
362 list <- strsplit(list, ",")
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guerler
parents:
diff changeset
363 if (length(list) > 0) {
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guerler
parents:
diff changeset
364 list <- list[[1]]
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guerler
parents:
diff changeset
365 for (entry in list) {
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guerler
parents:
diff changeset
366 pair <- strsplit(entry, ":")
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guerler
parents:
diff changeset
367 if (length(pair) > 0) {
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guerler
parents:
diff changeset
368 pair <- pair[[1]]
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guerler
parents:
diff changeset
369 if (length(pair) == 2) {
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guerler
parents:
diff changeset
370 options[[pair[1]]] <- pair[2]
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guerler
parents:
diff changeset
371 }
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guerler
parents:
diff changeset
372 }
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guerler
parents:
diff changeset
373 }
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guerler
parents:
diff changeset
374 }
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guerler
parents:
diff changeset
375 return(options)
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guerler
parents:
diff changeset
376 }
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guerler
parents:
diff changeset
377
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guerler
parents:
diff changeset
378 # get options, using the spec as defined by the enclosed list.
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guerler
parents:
diff changeset
379 spec = matrix(c(
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parents:
diff changeset
380 'workdir', 'w', 1, 'character', 'Work directory',
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guerler
parents:
diff changeset
381 'module', 'm', 1, 'character', 'Module name',
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guerler
parents:
diff changeset
382 'input', 'i', 1, 'character', 'Input tabular file',
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guerler
parents:
diff changeset
383 'columns', 'c', 1, 'character', 'Columns string',
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guerler
parents:
diff changeset
384 'settings', 's', 1, 'character', 'Settings string',
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guerler
parents:
diff changeset
385 'output', 'o', 1, 'character', 'Output tabular file',
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guerler
parents:
diff changeset
386 'help', 'h', 0, '', 'Help',
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guerler
parents:
diff changeset
387 'verbose', 'v', 0, '', 'Verbose'
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guerler
parents:
diff changeset
388 ), byrow=TRUE, ncol=5);
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guerler
parents:
diff changeset
389 opt = getopt(spec);
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guerler
parents:
diff changeset
390
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guerler
parents:
diff changeset
391 # show help
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guerler
parents:
diff changeset
392 if ( !is.null(opt$help) ||
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guerler
parents:
diff changeset
393 is.null(opt$module) ||
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guerler
parents:
diff changeset
394 is.null(opt$input) ||
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guerler
parents:
diff changeset
395 is.null(opt$columns) ||
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guerler
parents:
diff changeset
396 is.null(opt$output)) {
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guerler
parents:
diff changeset
397 cat(getopt(spec, usage=TRUE))
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guerler
parents:
diff changeset
398 q(status=1);
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guerler
parents:
diff changeset
399 }
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guerler
parents:
diff changeset
400
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guerler
parents:
diff changeset
401 # read columns/settings
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guerler
parents:
diff changeset
402 columns = split(opt$columns)
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guerler
parents:
diff changeset
403 settings = split(opt$settings)
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guerler
parents:
diff changeset
404
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guerler
parents:
diff changeset
405 # read table
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guerler
parents:
diff changeset
406 table <- read.table(opt$input)
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guerler
parents:
diff changeset
407
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guerler
parents:
diff changeset
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$columns, sep=' ')
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423
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424 # fill gaps
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425 if (length(l) > 0) {
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426 # print details
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427 if (!is.null(opt$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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434 }
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435
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436 # create output file
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437 output <- file(opt$output, open='wt')
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438
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439 # write header
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440 writeLines('#', output)
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441 writeLines(header_title, output)
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442 writeLines(header_date, output)
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443 writeLines(header_module, output)
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444 writeLines(header_settings, output)
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445 writeLines(header_columns, output)
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446 writeLines('#', output)
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447
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448 # write table
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449 write.table(l, file=output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
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450
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451 # close file
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452 close(output)
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453 } else {
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454 print ('Columns:')
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455 print (columns)
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456 print ('Settings:')
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457 print (settings)
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458 print ('No output generated.')
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459 }