diff report_clonality/r_wrapper.sh @ 26:28fbbdfd7a87 draft

Uploaded

--- a/report_clonality/r_wrapper.sh	Thu Feb 09 07:20:09 2017 -0500
+++ b/report_clonality/r_wrapper.sh	Mon Feb 13 09:08:46 2017 -0500
@@ -222,54 +222,40 @@
 	
 	for sample in $samples; do
 		echo "${clonality_method}"
-		if [[ "${clonality_method}" == "old" ]] ; then
-			echo "in old"
-			clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
-			echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
-			
-			if [[ "${clonality_method}" == "boyd" ]] ; then
-				echo "<thead><tr><th colspan='2'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile
-			fi
-
-			#replicate,reads,squared
-			echo "<tr><td>Replicate ID</td><td>Number of Sequences</td></tr>" >> $outputFile
-			while IFS=, read replicate reads squared
-			do
-				echo "<tr><td>$replicate</td><td>$reads</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></tr>" >> $outputFile
-			done < $outputDir/ReplicateSumReads_$sample.csv
-			
-			echo "<tr><td></td><td></td></tr>" >> $outputFile
-			
-			#overview
-			echo "<tr><td>Number of replicates containing the coincidence</td><td>Number of sequences shared between replicates</td></tr>" >> $outputFile
-			while IFS=, read type count weight weightedCount
-			do
-				if [[ "$type" -eq "1" ]]; then
-					echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
-				else
-					echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile
-				fi
-				
-			done < $outputDir/ClonalityOverView_$sample.csv
-			echo "</table></div>" >> $outputFile
-		else
-			echo "in new"
+		
+		echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
+		
+		if [[ "${clonality_method}" == "boyd" ]] ; then
 			clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)"
-			echo "<div class='tabbertab' title='$sample'>" >> $outputFile
-			echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile
-			echo "<table border = 1>" >> $outputFile
-			while read type count
-			do
-				echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
-			done < $outputDir/lymphclon_coincidences_$sample.txt
-			echo "</table></div>" >> $outputFile
+            echo "<tr><td>Clonality Score: </td><td>$clonalityScore</td></tr>" >> $outputFile
 		fi
+		
+		#replicate,reads,squared
+        echo "<tr><td>Replicate ID</td><td>Number of Sequences</td></tr>" >> $outputFile
+        while read replicate reads squared
+        do
+            echo "<tr><td>$replicate</td><td>$reads</td></tr>" >> $outputFile
+        done < $outputDir/ReplicateReads_$sample.txt
+        
+        #sum of reads and reads squared
+        while read readsSum squaredSum
+            do
+                echo "<tr><td>Sum</td><td>$readsSum</td></tr>" >> $outputFile
+        done < $outputDir/ReplicateSumReads_$sample.txt
+        
+        echo "<tr><td></td><td></td></tr>" >> $outputFile
+        
+        #overview
+        echo "<tr><td>Number of replicates containing the coincidence</td><td>Number of sequences shared between replicates</td></tr>" >> $outputFile
+        while read type count weight weightedCount
+        do
+            if [[ "$type" -eq "1" ]]; then
+                echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
+            else
+                echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile
+            fi
+        done < $outputDir/ClonalityOverView_$sample.txt
+        echo "</table></div>" >> $outputFile
 	done
 	
 	cat $dir/naive_clonality.htm >> $outputFile
@@ -295,7 +281,7 @@
 	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
-		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
+		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_mean_wD.txt
 	echo "</tbody></table>" >> $outputFile
 	
@@ -309,7 +295,7 @@
 	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
-		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
+		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_median_wD.txt
 	echo "</tbody></table>" >> $outputFile
 	
@@ -325,7 +311,7 @@
 	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
 	do
-		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
+		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_mean_nD.txt
 	echo "</tbody></table>" >> $outputFile
 	
@@ -339,7 +325,7 @@
 	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
 	do
-		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
+		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-/td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_median_nD.txt
 	echo "</tbody></table>" >> $outputFile