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4
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1 #!/usr/bin/Rscript
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2
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35
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3 # load getopt library
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4 library('getopt');
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4
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5
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6 # convert multi parameter string (i.e. key1: value, key2: value, ...) to object
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7 split <- function(argument){
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8 # process parameter string
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9 options <- list()
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10 list <- gsub("\\s","", argument)
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11 list <- strsplit(list, ",")
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12 if (length(list) > 0) {
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13 list <- list[[1]]
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14 for (entry in list) {
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15 pair <- strsplit(entry, ":")
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16 if (length(pair) > 0) {
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17 pair <- pair[[1]]
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18 if (length(pair) == 2) {
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19 options[[pair[1]]] <- pair[2]
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20 }
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21 }
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22 }
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23 }
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24 return(options)
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25 }
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26
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27 # get options, using the spec as defined by the enclosed list.
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28 spec = matrix(c(
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29 'workdir', 'w', 1, 'character', 'Work directory',
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30 'module', 'm', 1, 'character', 'Module name',
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31 'input', 'i', 1, 'character', 'Input tabular file',
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32 'columns', 'c', 1, 'character', 'Columns string',
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33 'settings', 's', 1, 'character', 'Settings string',
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34 'output', 'o', 1, 'character', 'Output tabular file',
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35 'help', 'h', 0, '', 'Help',
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36 'verbose', 'v', 0, '', 'Verbose'
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37 ), byrow=TRUE, ncol=5);
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38 opt = getopt(spec);
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39
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40 # show help
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41 if ( !is.null(opt$help) ||
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42 is.null(opt$module) ||
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43 is.null(opt$input) ||
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44 is.null(opt$columns) ||
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45 is.null(opt$output)) {
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46 cat(getopt(spec, usage=TRUE))
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47 q(status=1);
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48 }
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49
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50 # read columns/settings
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51 columns = split(opt$columns)
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52 settings = split(opt$settings)
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53
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54 # read table
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55 table <- read.table(opt$input)
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56
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57 # identify module file
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58 module_file = paste(opt$workdir, opt$module, '.r', sep='')
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59
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60 # source module
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61 source(module_file)
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62
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63 # run module
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64 l = wrapper (table, columns, settings)
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65
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66 # header
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67 header_title <- '# title - Chart Utilities (charts)'
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68 header_date <- paste('# date -', Sys.time(), sep=' ')
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69 header_module <- paste('# module -', opt$module, sep=' ')
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70 header_settings <- paste('# settings -', opt$settings, sep=' ')
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71 header_columns <- paste('# columns -', opt$columns, sep=' ')
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72
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35
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73 # check result
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4
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74 if (length(l) > 0) {
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75 # print details
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76 if (!is.null(opt$verbose)) {
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77 print ('Columns:')
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78 print (columns)
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79 print ('Settings:')
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80 print (settings)
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81 print ('Result:')
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82 print (l)
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83 }
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84
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85 # create output file
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86 output <- file(opt$output, open='wt')
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87
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88 # write header
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89 writeLines('#', output)
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90 writeLines(header_title, output)
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91 writeLines(header_date, output)
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92 writeLines(header_module, output)
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93 writeLines(header_settings, output)
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94 writeLines(header_columns, output)
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95 writeLines('#', output)
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96
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59
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97 # pad columns
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98 rows <- max(unlist(lapply(l, length)))
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99 padded <- lapply(l, function(col) {
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100 length(col) = rows;
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101 col
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102 })
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103
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4
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104 # write table
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59
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105 write.table(padded, file=output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
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4
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106
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107 # close file
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108 close(output)
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109 } else {
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35
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110 # print details
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4
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111 print ('Columns:')
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112 print (columns)
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113 print ('Settings:')
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114 print (settings)
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115 print ('No output generated.')
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116 } |
