Mercurial > repos > davidvanzessen > imgt_immunerepertoire_igg

diff combined.sh @ 0:3cce6e04b1e8 draft

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author davidvanzessen
date Thu, 23 Jan 2014 08:35:31 -0500
parents
children 8b026af4b298
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combined.sh	Thu Jan 23 08:35:31 2014 -0500
@@ -0,0 +1,106 @@
+#!/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
+
+
+
+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 $outputDir/samples.txt`
+count=1
+echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
+hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
+for sample in $samples; do
+	clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
+	echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
+	echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
+
+	echo "$hasReplicateColumn"
+	#if its a 'new' merged file with replicate info
+	if [[ "$hasReplicateColumn" == "Yes" ]] ; then
+		echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
+
+		#replicate,reads,squared
+		echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
+		while IFS=, read replicate reads squared
+		do
+
+			echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
+		done < $outputDir/ReplicateReads_$sample.csv
+
+		#sum of reads and reads squared
+		while IFS=, read readsSum squaredSum
+			do
+				echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
+		done < $outputDir/ReplicateSumReads_$sample.csv
+
+		echo "</table></td></tr>" >> $outputFile
+
+		#overview
+		echo "<tr><td colspan='3'><table border='1'><tr><th>Coincidence Type</th><th>Raw Coincidence Freq</th><th>Coincidence Weight</th><th>Coincidences, Weighted</th></tr>" >> $outputFile
+		while IFS=, read type count weight weightedCount
+		do
+			echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
+		done < $outputDir/ClonalityOverView_$sample.csv
+		echo "</table></td></tr>" >> $outputFile
+	fi
+
+	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 "</html>" >> $outputFile