diff r_wrapper.sh @ 27:f919965e8816 draft

Uploaded

--- a/r_wrapper.sh	Mon Feb 09 08:53:30 2015 -0500
+++ b/r_wrapper.sh	Fri Mar 06 09:59:53 2015 -0500
@@ -7,6 +7,7 @@
 species=$5
 locus=$6
 filterproductive=$7
+clonality_method=$8
 dir="$(cd "$(dirname "$0")" && pwd)"
 useD="false"
 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
@@ -22,9 +23,10 @@
 		useD="false"
 	fi
 fi
+useD="false"
 mkdir $3
 cp $dir/genes.txt $outputDir
-Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive 2>&1
+Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1
 cp $dir/tabber.js $outputDir
 cp $dir/style.css $outputDir
 cp $dir/script.js $outputDir
@@ -89,34 +91,49 @@
 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
 echo "$hasReplicateColumn"
 #if its a 'new' merged file with replicate info
-if [[ "$hasReplicateColumn" == "Yes" ]] ; then
+if [[ "$hasReplicateColumn" == "Yes" && "$clonalType" != "none" ]] ; then
 	echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
 	for sample in $samples; do
-		clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
-		echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
-		echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
+		echo "${clonality_method}"
+		if [[ "${clonality_method}" == "old" ]] ; then
+			echo "in old"
+			clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
+			echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
+			echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
 
-		#replicate,reads,squared
-		echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
-		while IFS=, read replicate reads squared
-		do
+			#replicate,reads,squared
+			echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
+			while IFS=, read replicate reads squared
+			do
+				
+				echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
+			done < $outputDir/ReplicateReads_$sample.csv
 			
-			echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
-		done < $outputDir/ReplicateReads_$sample.csv
-		
-		#sum of reads and reads squared
-		while IFS=, read readsSum squaredSum
+			#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
+			
+			#overview
+			echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
+			while IFS=, read type count weight weightedCount
 			do
-				echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
-		done < $outputDir/ReplicateSumReads_$sample.csv
-		
-		#overview
-		echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></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></div>" >> $outputFile
+				echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
+			done < $outputDir/ClonalityOverView_$sample.csv
+			echo "</table></div>" >> $outputFile
+		else
+			echo "in new"
+			clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)"
+			echo "<div class='tabbertab' title='$sample'>" >> $outputFile
+			echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile
+			echo "<table border = 1>" >> $outputFile
+			while IFS=, read type count
+			do
+				echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
+			done < $outputDir/lymphclon_coincidences_$sample.csv
+			echo "</table></div>" >> $outputFile
+		fi
 	done
 	echo "</div></div>" >> $outputFile
 fi