comparison r_wrapper.sh @ 3:e96fe8edc9c6 draft

Uploaded

2:f8f74848443e

hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"

if [[ "$hasReplicateColumn" == "Yes" ]] ; then
	echo "<table border='1'><th><td>Sample</td><td>unique</td><td>VH.DEL</td><td>P1</td><td>N1</td><td>P2</td><td>DEL.DH</td><td>DH.DEL</td><td>P3</td><td>N2</td><td>P4</td><td>DEL.JH</td><td>Total.Del</td><td>Total.N</td><td>Total.P</td></th>" >> $outputFile
	while IFS=, read Sample unique VH.DEL P1 N1 P2 DEL.DH DH.DEL P3 N2 P4 DEL.JH Total.Del Total.N Total.P
	do
		echo "<tr><td>$Sample</td><td>$unique</td><td>$VH.DEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DEL.DH</td><td>$DH.DEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DEL.JH</td><td>$Total.Del</td><td>$Total.N</td><td>$Total.P</td></tr>" >> $outputFile
	done < $outputDir/junctionAnalysis.csv
	echo "</table>" >> $outputFile
fi

samples=`cat $outputDir/samples.txt`

3:e96fe8edc9c6

hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"

if [[ "$hasReplicateColumn" == "Yes" ]] ; then
	echo "<table border='1'><th><td>Sample</td><td>unique</td><td>VH.DEL</td><td>P1</td><td>N1</td><td>P2</td><td>DEL.DH</td><td>DH.DEL</td><td>P3</td><td>N2</td><td>P4</td><td>DEL.JH</td><td>Total.Del</td><td>Total.N</td><td>Total.P</td></th>" >> $outputFile
	while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
	do
		echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
	done < $outputDir/junctionAnalysis.csv
	echo "</table>" >> $outputFile
fi

samples=`cat $outputDir/samples.txt`