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10
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1 #Setup R error handling to go to stderr
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2 options( show.error.messages = FALSE, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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3
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4 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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5 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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6
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7 suppressMessages(library('getopt'))
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8
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9 #get options, using the spec as defined by the enclosed list.
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10 #we read the options from the default: commandArgs(TRUE).
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11 spec = matrix(c(
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12 'help' , 'h', 0, "logical",
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13 'input', 'i', 1, "character",
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14 'transcript', 't', 1, "character",
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15 'method', 'm', 2, "character",
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16 'cutoff', 'c', 2, "double",
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17 'type', 'p', 2, "character",
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18 'output', 'o', 1, "character"
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19 ), byrow=TRUE, ncol=4);
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20
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21 opt = getopt(spec);
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22
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23 suppressMessages(require(RNAprobR))
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24
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25 #Read and convert input to GRanges object
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26 data <- read.table(opt$input, header = TRUE)
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27 dataGR <- norm_df2GR(data)
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28
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29 #Check if given transcript exists in input file
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30 if ( ! opt$transcript %in% data$RNAid ) { stop("Transript not found. Check input file.") }
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31
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32 pdf(opt$output)
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33 for (method in strsplit(opt$method, ",")[[1]] ) {
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34
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35 #Check if columns exists in data file
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36 if (! method %in% colnames(data)) { next }
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37
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38 plotRNA(dataGR, opt$transcript, method, stat_cutoff = opt$cutoff, type = opt$type,
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39 main=paste(opt$transcript,": ", method, sep=""))
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40 }
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41 dev.off()
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