Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 40:106275b54470 draft

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Uploaded
author davidvanzessen
date Tue, 30 May 2017 07:26:33 -0400
parents b6936fb52ab9
children 1d8728f3ff37
comparison
equal deleted inserted replaced
39:bad6a9a53ae7 40:106275b54470
40 echo "<thead><tr><th>Donor/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2 40 echo "<thead><tr><th>Donor/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
41 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un 41 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
42 do 42 do
43 echo "<tr><td>$sample</td>" >> $2 43 echo "<tr><td>$sample</td>" >> $2
44 echo "<td>$all</td>" >> $2 44 echo "<td>$all</td>" >> $2
45 echo "<td>$productive (${perc_prod}%)</td>" >> $2 45 if [[ "$productive" != "0" ]] ; then
46 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2 46 echo "<td>$productive (${perc_prod}%)</td>" >> $2
47 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2 47 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2
48 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2 48 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2
49 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2
50 else
51 echo "<td colspan='4' style='background-color: red;'>No productive sequences!</td>" >> $2
52 fi
49 done < $outputDir/productive_counting.txt 53 done < $outputDir/productive_counting.txt
50 echo "</table><br />" >> $2 54 echo "</table><br />" >> $2
51 echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate. <br />" >> $2 55 echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate. <br />" >> $2
52 echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2 56 echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2
53 echo "</center></html>" >> $2 57 echo "</center></html>" >> $2