diff QDNAseq.sh @ 72:fb2dfd8ba417 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/QDNAseq.sh	Fri Sep 05 11:10:27 2014 -0400
@@ -0,0 +1,148 @@
+#!/bin/sh
+
+## This script creates a config file for use with the QDNAseq R wrapper
+## For use outside Galaxy
+
+QDNASEQ_R_SCRIPT='/ccagc/home/stef/code/QDNASEQ/QDNAseq.R'
+R_LOCATION='/ccagc/lib/R/R-3.1.0/bin/'
+OUTPUT_DIR='QDNASEQ'
+SCRIPT_DIR=$(dirname $0)
+SCRIPT_NAME=$(basename $0)
+
+binSizesString='1000,100,15'
+outputName=`basename $PWD`
+doSegment='TRUE'
+debug='FALSE'
+
+usage()
+{
+cat<<EOF
+  This script creates a QDNAseq wrapper config.
+  
+  Experiment name and/or output dir are optional
+    $SCRIPT_NAME [-n myExperiment] [-o outputDir] *.bam
+
+  Debug mode for working with build in LGG150 data
+    $SCRIPT_NAME -d
+
+  OPTIONS:
+    -n [s]  provide analysis name [$outputName]
+    -o [s]  output dir [$OUTPUT_DIR]
+    -d      debug mode (only create config)
+    
+EOF
+}
+
+PARAM_COUNT=0
+if [ $# -eq 0 ] || [ "$1" == "-h" ]
+then
+	usage
+	exit 1
+else
+	while getopts "n:o:d" opt; do
+	  case $opt in
+	    n)
+	      #echo "$opt was triggered, Parameter: $OPTARG" >&2
+	      outputName=$OPTARG
+	      PARAM_COUNT=`bc <<< $PARAM_COUNT+2`
+	      ;;
+	    o)
+	      OUTPUT_DIR=$OPTARG
+	      PARAM_COUNT=`bc <<< $PARAM_COUNT+2`
+	      ;;
+	    d)
+	      debug='TRUE'
+	      PARAM_COUNT=`bc <<< $PARAM_COUNT+1`
+	      ;;
+	    \?)
+	      echo "Invalid option: -$OPTARG" >&2
+	      exit 1
+	      ;;
+	    :)
+	      echo "Option -$OPTARG requires an argument." >&2
+	      exit 1
+	      ;;
+	  esac
+	done
+fi
+
+## set param dependent variables
+printf '%s\n' "[INFO] --- QDNAseq wrapper config creator ---"
+CONFIG_FILE=$OUTPUT_DIR'/qdnaseqConfig.R'
+
+## remove the params from input string leaving only the BAMs
+shift $PARAM_COUNT
+
+## sanity checks
+if [ -e $CONFIG_FILE ]; then
+	echo "[ERR] Config file ($CONFIG_FILE) already exists, exit.."; 
+	exit 0
+fi
+if [ -d $OUTPUT_DIR ]; then
+	echo "[ERR] Output dir ($OUTPUT_DIR) already exists, exit.."; 
+	exit 0
+else
+	mkdir $OUTPUT_DIR
+fi
+
+## variables setup
+CONFIG_TXT="## ==========
+## QDNAseq pipeline config file
+## ==========
+
+## ----------
+inGalaxy <- FALSE
+binSizesString <- '$binSizesString'
+experimentType <- 'SR50'
+outputName <- '$outputName'
+
+## ----------
+outputHtml  <- 'galaxyIndex.html'
+outputId    <- NA
+newFilePath <- '$OUTPUT_DIR'
+outputPath  <- '$OUTPUT_DIR'
+doSegment   <- as.logical( $doSegment )
+debug       <- as.logical( $debug )
+undoSD      <- as.double( 1.0 )
+binAnnotations <- ''
+
+## ----------
+filterBlacklistedBins <- as.logical( 'TRUE' )
+mappabilityCutoff <- as.integer( 0 )
+undoSplits <- 'sdundo'
+doOutputCopynumbersIgv <- FALSE
+
+## ----------
+PLOT_WIDTH <- as.integer( 1440 )
+PLOT_HEIGHT <- as.integer( 720 )
+excludeChrsString <- 'X,Y'
+
+## ----------
+bamsPaths <- c()
+bamsNames <- c()
+"
+
+## create config file
+printf '%s\n' "$CONFIG_TXT" > $CONFIG_FILE
+
+## add bam files to config file
+BAMS=$@
+for bam_path in $BAMS; do
+	
+	if [ ! -e $bam_path  ]; then
+		echo "[ERR] Bam file does not exist ($bam_path), exit.."; 
+		exit 0
+	fi
+
+	bam_name=`basename "$bam_path"`
+	printf '%s\n' "bamsPaths <- c( bamsPaths, \"$bam_path\" )" >> $CONFIG_FILE
+	printf '%s\n' "bamsNames <- c( bamsNames, \"$bam_name\" )" >> $CONFIG_FILE
+	printf '%s\n' "[INFO] BAM: $bam_name"
+done
+
+## done
+printf '%s\n' "[INFO] OUTPUT DIR:  $OUTPUT_DIR"
+printf '%s\n' "[INFO] OUTPUT NAME: $outputName"
+printf '%s\n' "[INFO] CONFIG FILE can be found in $CONFIG_FILE"
+printf '%s\n' "[INFO] Run with: $R_LOCATION/Rscript $QDNASEQ_R_SCRIPT $CONFIG_FILE"
+printf '%s\n' "[INFO] Done"
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