comparison report_clonality/r_wrapper.sh @ 64:55f18bf19d72 draft

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63:bd6fb6c03948

			#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

			
			#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>" >> $outputFile
		else
			echo "in new"
			clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)"

64:55f18bf19d72

			#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

			
			#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>" >> $outputFile
		else
			echo "in new"
			clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)"