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1 #!/usr/bin/env Rscript
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2
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3 #sink(file("/dev/null", "w"), type = "message");
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4
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5 library(affy)
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6 library(GEOquery);
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7 library(pathprint);
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8
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9 # Figure out the relative path to the galaxy-pathprint.r library.
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10 script.args <- commandArgs(trailingOnly = FALSE);
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11 script.name <- sub("--file=", "", script.args[grep("--file=", script.args)])
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12 script.base <- dirname(script.name)
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13 library.path <- file.path(script.base, "galaxy-pathprint.r");
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14 source(library.path)
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15
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16 data(GEO.metadata.matrix);
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17
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18 usage <- function() {
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19 sink(stderr(), type = "message");
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20 stop("Usage: fingerprint.r [ARGS]", call. = FALSE)
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21 }
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22
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23 ## Get the command line arguments.
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24 args <- commandArgs(trailingOnly = TRUE)
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25
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26 type <- ifelse(! is.na(args[1]), args[1], usage())
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27
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28 if (type == "geo") {
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29 geoID <- ifelse(! is.na(args[2]), args[2], usage());
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30 output <- ifelse(! is.na(args[3]), args[3], usage());
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31
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32 fingerprint <- generateFingerprint(geoID);
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33 } else if (type == "cel") {
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34 input <- ifelse(! is.na(args[2]), args[2], usage());
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35 output <- ifelse(! is.na(args[3]), args[3], usage());
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36
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37 fingerprint <- loadFingerprintFromCELFile(input);
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38 } else if (type == "expr") {
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39 input <- ifelse(! is.na(args[2]), args[2], usage());
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40 platform <- ifelse(! is.na(args[3]), args[3], usage());
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41 output <- ifelse(! is.na(args[4]), args[4], usage());
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42
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43 fingerprint <- loadFingerprintFromExprsFile(input, platform);
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44 } else {
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45 usage();
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46 };
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47
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48 saveFingerprint(fingerprint, output);
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49
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50 quit("no", 0)
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