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1 #!/usr/bin/Rscript
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2
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3 ## --------------------
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4 ## prints all arguments as msg
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5 ## --------------------
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6 catMsg <- function( msg=c() ){
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7 cat( MAIN_NAME, paste( msg, collapse="" ), "\n", sep='')
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8 }
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9
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10 ## ==================================================
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11 ## Start of analysis
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12 ## ==================================================
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13 MAIN_NAME <- '[INFO] '
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14 catMsg( "Starting QDNAseq-export wrapper" )
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15
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16 ## supress msg to allow R to finish with non-error msg
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17 catMsg( "Loading R libraries" )
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18 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
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19 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
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20
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21 ## only one param: the tmp config file
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22 cmdLineArgs <- commandArgs(TRUE)
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23 config <- cmdLineArgs[1]
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24
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25 ## sourcing the config file will load all input params
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26 ## many variables are imported via sourced "config"
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27 source( config ) # outputFile, outputName, outputFormat, sampleIndex, filterBins
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28
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29 systemUser <- system("whoami",T)
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30 qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
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31 rVersion <- R.version.string
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32 rPath <- R.home()
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33 catMsg( c("QDNAseq version ", qdnaseqVersion) )
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34 catMsg( c( rVersion ) )
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35 qdnaseqObject <- readRDS( rdsFilePath )
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36 logTransform <- TRUE
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37
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38 sampleNames <- sampleNames( qdnaseqObject )
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39 elements <- assayDataElementNames(qdnaseqObject)
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40 element <- dataLevel
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41 if (dataLevel == "segments") element <- "segmented"
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42 if (element == "calls") logTransform <- FALSE
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43
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44 ## sanity checks
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45 if ( ! element %in% elements ) stop( paste( "Data-level \"", element, "\" not present in object", sep='') )
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46 if ( outputFormat == "bed" ){
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47 if ( sampleIndex == "None") stop("Bed option requires sample index")
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48 if ( sampleIndex > length(sampleNames) ) stop("Chosen sample index not present in object")
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49 qdnaseqObject <- qdnaseqObject[ ,sampleIndex]
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50 }
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51
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52 ## output
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53 exportBins( qdnaseqObject,
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54 file=outputFile,
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55 format=outputFormat,
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56 filter=filterBins,
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57 type=dataLevel,
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58 logTransform=logTransform
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59 )
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60
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61 ## tell galaxy all seems ok
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62 q(status=0)
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