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1 # ImmPort FCSKeywords
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2 ######################################################################
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3 # Copyright (c) 2016 Northrop Grumman.
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4 # All rights reserved.
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5 ######################################################################
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6 #
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7 # Converts the FCS file to text without transformaton
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8 # To run in R
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9 # 1) library(flowCore)
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10 # 2) source("FCSKeyword.R")
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11 # 3) transformFCS("filename")
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12 #
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13 # Version 1.4.1
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14 # March 2016 -- added lines to run directly from command line
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15 #
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16
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17 library(flowCore)
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18
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19 #
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20 # Starting function for processing a FCS file
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21 #
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22 extractKeywords <- function(input_file, keyword_file="", debug=FALSE) {
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23 #
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24 # Generate the file names for the output_file and keyword_file
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25 #
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26 pieces <- unlist(strsplit(input_file, .Platform$file.sep))
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27 filename <- pieces[length(pieces)]
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28
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29 if (keyword_file == "") {
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30 filepieces <- unlist(strsplit(filename, '\\.'))
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31 #replace .fcs with .keyword; append .keyword if not ending in .fcs
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32 if (filepieces[length(filepieces)] == 'fcs') {
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33 filepieces[length(filepieces)] = 'keyword'
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34 } else {
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35 filepieces[length(filepieces)+1] = 'keyword'
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36 }
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37 keyword_file <- paste(filepieces, collapse = '.')
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38 }
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39
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40 if (debug) {
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41 print (paste("Converting file: ", input_file))
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42 print (paste("Original file name: ", filename))
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43 print (paste("Output file name: ", output_file))
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44 print (paste("Keyword file name: ", keyword_file))
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45 }
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46 fcs <- read.FCS(input_file, transformation=F)
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47 keywords <- keyword(fcs)
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48 write.table(as.matrix(keywords), file=keyword_file, quote=F,
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49 row.names=T, col.names=F, sep='=', append=F)
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50 }
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51
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52 # Extract Keywords
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53 # @param input_file FCS file to be transformed
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54 # @param keyword_file FCS file keywords ".keywords" extension"
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55 transformFCS <- function(input_file, keyword_file="", debug=FALSE) {
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56 isValid <- F
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57 # Check file beginning matches FCS standard
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58 tryCatch({
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59 isValid = isFCSfile(input_file)
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60 }, error = function(ex) {
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61 print (paste(" ! Error in isFCSfile", ex))
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62 })
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63
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64 if (isValid) {
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65 extractKeywords(input_file, keyword_file, debug)
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66 } else {
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67 print (paste(input_file, "does not meet FCS standard"))
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68 }
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69 }
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70
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71 args <- commandArgs(TRUE)
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72 transformFCS(args[2], args[3])
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