Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/r_wrapper.sh @ 47:d97e1421aa86 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 27 Jan 2016 10:25:43 -0500 |
| parents | fee06348bfad |
| children | d08dfc8d5225 |
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--- a/report_clonality/r_wrapper.sh Wed Jan 27 08:39:16 2016 -0500 +++ b/report_clonality/r_wrapper.sh Wed Jan 27 10:25:43 2016 -0500 @@ -8,6 +8,7 @@ locus=$6 filterproductive=$7 clonality_method=$8 +filter_uniques=$9 dir="$(cd "$(dirname "$0")" && pwd)" useD="false" if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then @@ -25,7 +26,7 @@ fi mkdir $3 cp $dir/genes.txt $outputDir -Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1 +Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} ${filter_uniques} 2>&1 cp $dir/tabber.js $outputDir cp $dir/style.css $outputDir cp $dir/script.js $outputDir @@ -34,11 +35,12 @@ echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $2 echo "<table border = 1>" >> $2 -echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2 -while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un +echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Removed</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2 +while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un removed perc_rem do echo "<tr><td>$sample</td>" >> $2 echo "<td>$all</td>" >> $2 + echo "<td>${removed} (${perc_rem}%)</td>" >> $2 echo "<td>$productive (${perc_prod}%)</td>" >> $2 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2