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comparison chartskit.r @ 1:b4722f9d496f draft

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author guerler
date Mon, 31 Mar 2014 17:22:09 -0400
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children 4aeb334de0e3
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0:a6a023d1fa11 1:b4722f9d496f
1 #!/usr/bin/Rscript
2
3 # convert multi parameter string (i.e. key1: value, key2: value, ...) to object
4 split <- function(argument){
5 # process parameter string
6 options <- list()
7 list <- gsub("\\s","", argument)
8 list <- strsplit(list, ",")
9 if (length(list) > 0) {
10 list <- list[[1]]
11 for (entry in list) {
12 pair <- strsplit(entry, ":")
13 if (length(pair) > 0) {
14 pair <- pair[[1]]
15 if (length(pair) == 2) {
16 options[[pair[1]]] <- pair[2]
17 }
18 }
19 }
20 }
21 return(options)
22 }
23
24 # load package
25 if('getopt' %in% rownames(installed.packages()) == FALSE) {
26 install.packages('getopt', repos='http://cran.us.r-project.org')
27 }
28 library(getopt);
29
30 # get options, using the spec as defined by the enclosed list.
31 spec = matrix(c(
32 'module', 'm', 1, 'character', 'Module name',
33 'input', 'i', 1, 'character', 'Input tabular file',
34 'columns', 'c', 1, 'character', 'Columns string',
35 'settings', 's', 1, 'character', 'Settings string',
36 'output', 'o', 1, 'character', 'Output tabular file',
37 'help', 'h', 0, '', 'Help',
38 'verbose', 'v', 0, '', 'Verbose'
39 ), byrow=TRUE, ncol=5);
40 opt = getopt(spec);
41
42 # show help
43 if ( !is.null(opt$help) || is.null(opt$module) || is.null(opt$input) || is.null(opt$columns) || is.null(opt$output)) {
44 cat(getopt(spec, usage=TRUE));
45 q(status=1);
46 }
47
48 # read columns/settings
49 columns = split(opt$columns)
50 settings = split(opt$settings)
51
52 # read table
53 table <- read.table(opt$input)
54
55 # source module
56 source(opt$module)
57
58 # run module
59 l = wrapper (table, columns, settings)
60
61 # fill gaps
62 if (length(l) > 0) {
63 n <- max(sapply(l, length))
64 ll <- lapply(l, function(X) {
65 c(as.character(X), rep("", times = n - length(X)))
66 })
67 out <- do.call(cbind, ll)
68
69 # print details
70 if (!is.null(opt$verbose)) {
71 print ('Columns:')
72 print (columns)
73 print ('Settings:')
74 print (settings)
75 print ('Result:')
76 print (out)
77 }
78
79 # write table
80 write.table(out, file=opt$output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
81 } else {
82 print ('Columns:')
83 print (columns)
84 print ('Settings:')
85 print (settings)
86 print ('No output generated.')
87 }