Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

comparison combined.sh @ 7:e6f28d0a0f14 draft

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Uploaded
author davidvanzessen
date Fri, 22 Nov 2013 09:08:45 -0500
parents fc186246d291
children 8d83319a0f3d
comparison
equal deleted inserted replaced
6:fc186246d291 7:e6f28d0a0f14
66 echo "<img src='DPlot.png'/>" >> $outputFile 66 echo "<img src='DPlot.png'/>" >> $outputFile
67 echo "<img src='JPlot.png'/>" >> $outputFile 67 echo "<img src='JPlot.png'/>" >> $outputFile
68 68
69 samples=`cat $outputDir/samples.txt` 69 samples=`cat $outputDir/samples.txt`
70 count=1 70 count=1
71 echo "<table border='1'>" >> $outputFile 71 echo "<table border='1'><caption><h3>$clonalType</h3></caption>" >> $outputFile
72 for sample in $samples; do 72 for sample in $samples; do
73 echo "<tr><td colspan='3' height='100'></td>" >> $outputFile 73 echo "<tr><td colspan='3' height='100'></td>" >> $outputFile
74 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile 74 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
75 echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile 75 echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile
76 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" 76 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
80 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" 80 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
81 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile 81 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
82 count=$((count+1)) 82 count=$((count+1))
83 done 83 done
84 echo "</table>" >> $outputFile 84 echo "</table>" >> $outputFile
85 echo "<h1>$clonalType</h1>" >> $outputFile
86 85
87 echo "</html>" >> $2 86 echo "</html>" >> $2