comparison report_clonality/r_wrapper.sh @ 16:21ca9391a3b7 draft

Uploaded

15:02efa5764a0a

			clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
			echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
			echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile

			#replicate,reads,squared
			echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
			while IFS=, read replicate reads squared
			do
				echo "<tr><td>$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
				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>" >> $outputFile
			while IFS=, read type count weight weightedCount
			do
				if [[ "$type" -eq "1" ]]; then
					echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
				else
					echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
				fi
				
			done < $outputDir/ClonalityOverView_$sample.csv
			echo "</table></div>" >> $outputFile
		else

16:21ca9391a3b7

			clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
			echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
			echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile

			#replicate,reads,squared
			echo "<tr><td>Replicate ID</td><td>Number of Reads</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
			
			#overview
			echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</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