Mercurial > repos > davidvanzessen > argalaxy_tools
comparison report_clonality/r_wrapper.sh @ 22:c28da767799f draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 27 Jan 2017 04:24:41 -0500 |
| parents | 3ef457aa5df6 |
| children | e2fbdfacec1d |
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| 21:9c843eb06416 | 22:c28da767799f |
|---|---|
| 256 | 256 |
| 257 done < $outputDir/ClonalityOverView_$sample.csv | 257 done < $outputDir/ClonalityOverView_$sample.csv |
| 258 echo "</table></div>" >> $outputFile | 258 echo "</table></div>" >> $outputFile |
| 259 else | 259 else |
| 260 echo "in new" | 260 echo "in new" |
| 261 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)" | 261 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)" |
| 262 echo "<div class='tabbertab' title='$sample'>" >> $outputFile | 262 echo "<div class='tabbertab' title='$sample'>" >> $outputFile |
| 263 echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile | 263 echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile |
| 264 echo "<table border = 1>" >> $outputFile | 264 echo "<table border = 1>" >> $outputFile |
| 265 while IFS=, read type count | 265 while IFS=, read type count |
| 266 do | 266 do |
| 267 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile | 267 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile |
| 268 done < $outputDir/lymphclon_coincidences_$sample.csv | 268 done < $outputDir/lymphclon_coincidences_$sample.txt |
| 269 echo "</table></div>" >> $outputFile | 269 echo "</table></div>" >> $outputFile |
| 270 fi | 270 fi |
| 271 done | 271 done |
| 272 | 272 |
| 273 cat $dir/naive_clonality.htm >> $outputFile | 273 cat $dir/naive_clonality.htm >> $outputFile |