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1 #!/usr/bin/Rscript
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2
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3 # convert multi parameter string (i.e. key1: value, key2: value, ...) to object
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4 split <- function(argument){
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5 # process parameter string
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6 options <- list()
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7 list <- gsub("\\s","", argument)
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8 list <- strsplit(list, ",")
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9 if (length(list) > 0) {
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10 list <- list[[1]]
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11 for (entry in list) {
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12 pair <- strsplit(entry, ":")
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13 if (length(pair) > 0) {
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14 pair <- pair[[1]]
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15 if (length(pair) == 2) {
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16 options[[pair[1]]] <- pair[2]
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17 }
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18 }
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19 }
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20 }
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21 return(options)
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22 }
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23
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24 # load package
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25 if('getopt' %in% rownames(installed.packages()) == FALSE) {
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26 install.packages('getopt', repos='http://cran.us.r-project.org')
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27 }
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28 library(getopt);
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29
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30 # get options, using the spec as defined by the enclosed list.
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31 spec = matrix(c(
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32 'module', 'm', 1, 'character', 'Module name',
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33 'input', 'i', 1, 'character', 'Input tabular file',
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34 'columns', 'c', 1, 'character', 'Columns string',
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35 'settings', 's', 1, 'character', 'Settings string',
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36 'output', 'o', 1, 'character', 'Output tabular file',
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37 'help', 'h', 0, '', 'Help',
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38 'verbose', 'v', 0, '', 'Verbose'
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39 ), byrow=TRUE, ncol=5);
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40 opt = getopt(spec);
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41
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42 # show help
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43 if ( !is.null(opt$help) || is.null(opt$module) || is.null(opt$input) || is.null(opt$columns) || is.null(opt$output)) {
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44 cat(getopt(spec, usage=TRUE));
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45 q(status=1);
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46 }
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47
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48 # read columns/settings
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49 columns = split(opt$columns)
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50 settings = split(opt$settings)
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51
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52 # read table
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53 table <- read.table(opt$input)
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54
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55 # source module
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56 source(opt$module)
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57
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58 # run module
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59 l = wrapper (table, columns, settings)
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60
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61 # fill gaps
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62 if (length(l) > 0) {
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63 n <- max(sapply(l, length))
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64 ll <- lapply(l, function(X) {
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65 c(as.character(X), rep("", times = n - length(X)))
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66 })
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67 out <- do.call(cbind, ll)
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68
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69 # print details
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70 if (!is.null(opt$verbose)) {
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71 print ('Columns:')
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72 print (columns)
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73 print ('Settings:')
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74 print (settings)
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75 print ('Result:')
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76 print (out)
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77 }
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78
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79 # write table
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80 write.table(out, file=opt$output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
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81 } else {
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82 print ('Columns:')
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83 print (columns)
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84 print ('Settings:')
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85 print (settings)
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86 print ('No output generated.')
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87 } |
