Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 22:c28da767799f draft

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Uploaded
author davidvanzessen
date Fri, 27 Jan 2017 04:24:41 -0500
parents 3ef457aa5df6
children e2fbdfacec1d
comparison
equal deleted inserted replaced
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