comparison chartskit.r @ 31:7774e0097ff4 draft

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30:533b6c8f8584

    return(options)
}

# get options, using the spec as defined by the enclosed list.
spec = matrix(c(
    'module',   'm', 1, 'character', 'Module name',
    'input',    'i', 1, 'character', 'Input tabular file',
    'columns',  'c', 1, 'character', 'Columns string',
    'settings', 's', 1, 'character', 'Settings string',
    'output',   'o', 1, 'character', 'Output tabular file',

    'verbose',  'v', 0, '',          'Verbose'
), byrow=TRUE, ncol=5);
opt = getopt(spec);

# show help
if ( !is.null(opt$help) || is.null(opt$module) || is.null(opt$input) || is.null(opt$columns) || is.null(opt$output)) {
    cat(getopt(spec, usage=TRUE));
    q(status=1);
}

# read columns/settings
columns = split(opt$columns)
settings = split(opt$settings)

# read table
table <- read.table(opt$input)

# source module
source(opt$module)

# run module
l = wrapper (table, columns, settings)

# fill gaps
if (length(l) > 0) {
    n <- max(sapply(l, length))
    ll <- lapply(l, function(X) {
        c(as.character(X), rep("", times = n - length(X)))
    })
    out <- do.call(cbind, ll)

    # print details
    if (!is.null(opt$verbose)) {
        print ('Columns:')
        print (columns)
        print ('Settings:')
        print (settings)
        print ('Result:')
        print (out)
    }

    # write table
    write.table(out, file=opt$output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
} else {
    print ('Columns:')
    print (columns)
    print ('Settings:')
    print (settings)

31:7774e0097ff4

    return(options)
}

# get options, using the spec as defined by the enclosed list.
spec = matrix(c(
    'workdir',  'w', 1, 'character', 'Work directory',
    'module',   'm', 1, 'character', 'Module name',
    'input',    'i', 1, 'character', 'Input tabular file',
    'columns',  'c', 1, 'character', 'Columns string',
    'settings', 's', 1, 'character', 'Settings string',
    'output',   'o', 1, 'character', 'Output tabular file',

    'verbose',  'v', 0, '',          'Verbose'
), byrow=TRUE, ncol=5);
opt = getopt(spec);

# show help
if ( !is.null(opt$help) ||
    is.null(opt$module) ||
    is.null(opt$input) ||
    is.null(opt$columns) ||
    is.null(opt$output)) {
    cat(getopt(spec, usage=TRUE))
    q(status=1);
}

# read columns/settings
columns = split(opt$columns)
settings = split(opt$settings)

# read table
table <- read.table(opt$input)

# identify module file
module_file = paste(opt$workdir, opt$module, '.r', sep='')

# source module
source(module_file)

# run module
l = wrapper (table, columns, settings)

# header
header_title <- '# title\t\tCharts Toolkit (chartskit)'
header_date <- paste('# date\t\t', Sys.time(), sep='')
header_module <- paste('# module\t', opt$module, sep='')
header_settings <- paste('# settings\t', opt$settings, sep='')
header_columns <- paste('# columns\t', opt$columns, sep='')

# fill gaps
if (length(l) > 0) {
    # print details
    if (!is.null(opt$verbose)) {
        print ('Columns:')
        print (columns)
        print ('Settings:')
        print (settings)
        print ('Result:')
        print (l)
    }

    # create output file
    output <- file(opt$output, open='wt')
    
    # write header
    writeLines('#', output)
    writeLines(header_title, output)
    writeLines(header_date, output)
    writeLines(header_module, output)
    writeLines(header_settings, output)
    writeLines(header_columns, output)
    writeLines('#', output)
    
    # write table
    write.table(l, file=output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
    
    # close file
    close(output)
} else {
    print ('Columns:')
    print (columns)
    print ('Settings:')
    print (settings)