Mercurial > repos > davidvanzessen > combined_immune_repertoire_imgt

diff immunerepertoirecombined_imgt/combined.sh @ 0:e71c59b72669 draft

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author davidvanzessen
date Mon, 09 Dec 2013 03:45:21 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/immunerepertoirecombined_imgt/combined.sh	Mon Dec 09 03:45:21 2013 -0500
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+export IGDATA=/home/david/tmp/ncbi-igblast-1.0.0;
+
+clonalType=${@:(-3):1}
+html=${@:(-2):1}
+imageDir=${@:(-1):1}
+dataCount=`expr $# - 3`
+inputData=${@:(1):dataCount}
+dir="$(cd "$(dirname "$0")" && pwd)"
+array=("$@")
+echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
+echo "<tr><td>-----------------------------------</td></tr>" >> $html
+
+id=${inputData[0]}
+forwardSlash="/"
+mergerInput=()
+count=0
+for current in $inputData; do
+    if [[ "$current" != *"$forwardSlash"* ]]; then
+        id=$current
+        count=0
+        mergerInput+=($id)
+        continue
+    fi
+    fileName=$(basename $current)
+    convertedFileName="${fileName%.*}"
+    convertedFileName="$PWD/$convertedFileName.converted"
+	bash $dir/imgtconvert.sh $current $id $count $convertedFileName
+	mergerInput+=($convertedFileName)
+	count=$((count+1))
+done
+wait
+
+
+
+echo "<tr><td>-----------------------------------</td></tr>" >> $html
+echo "<tr><td>merging</td></tr>" >> $html
+
+python $dir/igblastmerge.py ${mergerInput[*]}  --output $PWD/merged.txt
+
+echo "<tr><td>done</td></tr>" >> $html
+echo "<tr><td>-----------------------------------</td></tr>" >> $html
+echo "<tr><td>plotting</td></tr>" >> $html
+
+
+inputFile=$PWD/merged.txt
+outputFile=$html
+outputDir=$imageDir
+mkdir $outputDir
+Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
+echo "<html>" > $outputFile
+echo "<img src='VPlot.png'/>" >> $outputFile
+echo "<img src='DPlot.png'/>" >> $outputFile
+echo "<img src='JPlot.png'/>" >> $outputFile
+
+samples=`cat $outputDir/samples.txt`
+count=1
+echo "<table border='1'>" >> $outputFile
+for sample in $samples; do
+	echo "<tr><td colspan='3' height='100'></td>" >> $outputFile
+	echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
+	echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile
+	mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
+	echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
+	mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
+	echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
+	mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
+	echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
+	count=$((count+1))
+done
+echo "</table>" >> $outputFile
+echo "<h1>$clonalType</h1>" >> $outputFile
+
+echo "</html>" >> $outputFile