| Previous changeset 15:02efa5764a0a (2016-12-20) Next changeset 17:da95be204ebc (2016-12-21) |
|
Commit message:
Uploaded |
|
modified:
report_clonality/r_wrapper.sh |
| b |
| diff -r 02efa5764a0a -r 21ca9391a3b7 report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Tue Dec 20 08:36:12 2016 -0500 +++ b/report_clonality/r_wrapper.sh Tue Dec 20 09:06:51 2016 -0500 |
| [ |
| @@ -193,26 +193,26 @@ 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 + 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>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile + echo "<tr><td>$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>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile + echo "<tr><td>Sum</td><td>$readsSum</td></tr>" >> $outputFile done < $outputDir/ReplicateSumReads_$sample.csv #overview - echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile + 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><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile + echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile else - echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile + echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile fi done < $outputDir/ClonalityOverView_$sample.csv |