diff QDNAseq-export.R @ 88:d2ea2b842c21 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/QDNAseq-export.R	Mon Jul 06 06:29:19 2015 -0400
@@ -0,0 +1,62 @@
+#!/usr/bin/Rscript
+
+## --------------------
+## prints all arguments as msg
+## --------------------
+catMsg <- function( msg=c() ){	
+	cat( MAIN_NAME, paste( msg, collapse="" ), "\n", sep='')
+}
+
+## ==================================================
+## Start of analysis
+## ==================================================
+MAIN_NAME <- '[INFO] '
+catMsg( "Starting QDNAseq-export wrapper" )
+
+## supress msg to allow R to finish with non-error msg
+catMsg( "Loading R libraries" )
+suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
+suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
+
+## only one param: the tmp config file
+cmdLineArgs <- commandArgs(TRUE)
+config      <- cmdLineArgs[1]
+
+## sourcing the config file will load all input params
+## many variables are imported via sourced "config"
+source( config ) # outputFile, outputName, outputFormat, sampleIndex, filterBins
+
+systemUser <- system("whoami",T)
+qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
+rVersion <- R.version.string
+rPath <- R.home()
+catMsg( c("QDNAseq version ", qdnaseqVersion) )
+catMsg( c( rVersion ) )
+qdnaseqObject <- readRDS( rdsFilePath )
+logTransform <- TRUE
+
+sampleNames <- sampleNames( qdnaseqObject )
+elements <- assayDataElementNames(qdnaseqObject)
+element <- dataLevel
+if (dataLevel == "segments") element <- "segmented"
+if (element == "calls") logTransform <- FALSE
+
+## sanity checks
+if ( ! element %in% elements ) stop( paste( "Data-level \"", element, "\" not present in object", sep='') ) 
+if ( outputFormat == "bed" ){
+	if ( sampleIndex == "None") stop("Bed option requires sample index")
+	if ( sampleIndex > length(sampleNames) ) stop("Chosen sample index not present in object")
+	qdnaseqObject <- qdnaseqObject[ ,sampleIndex]
+}
+
+## output
+exportBins( qdnaseqObject, 
+	file=outputFile, 
+	format=outputFormat, 
+	filter=filterBins, 
+	type=dataLevel, 
+	logTransform=logTransform 
+)
+
+## tell galaxy all seems ok
+q(status=0)