Mercurial > repos > davidvanzessen > report_clonality_igg

comparison r_wrapper.sh @ 1:81b9673b29be draft

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Uploaded
author davidvanzessen
date Tue, 28 Jan 2014 06:57:38 -0500
parents 08aa67564858
children f8f74848443e
comparison
equal deleted inserted replaced
0:08aa67564858 1:81b9673b29be
13 echo "<html>" >> $2 13 echo "<html>" >> $2
14 echo "<img src='VPlot.png'/>" >> $2 14 echo "<img src='VPlot.png'/>" >> $2
15 echo "<img src='DPlot.png'/>" >> $2 15 echo "<img src='DPlot.png'/>" >> $2
16 echo "<img src='JPlot.png'/>" >> $2 16 echo "<img src='JPlot.png'/>" >> $2
17 17
18 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
19
20 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
21 echo "<table border='1'><th><td>Sample</td><td>unique</td><td>VH.DEL</td><td>P1</td><td>N1</td><td>P2</td><td>DEL.DH</td><td>DH.DEL</td><td>P3</td><td>N2</td><td>P4</td><td>DEL.JH</td><td>Total.Del</td><td>Total.N</td><td>Total.P</td></th>" >> $outputFile
22 while IFS=, Sample unique VH.DEL P1 N1 P2 DEL.DH DH.DEL P3 N2 P4 DEL.JH Total.Del Total.N Total.P
23 do
24 echo "<tr><td>$Sample</td><td>$unique</td><td>$VH.DEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DEL.DH</td><td>$DH.DEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DEL.JH</td><td>$Total.Del</td><td>$Total.N</td><td>$Total.P</td></tr>" >> $outputFile
25 done < $outputDir/junctionAnalysis.csv
26 echo "</table>" >> $outputFile
27 fi
28
18 samples=`cat $outputDir/samples.txt` 29 samples=`cat $outputDir/samples.txt`
19 count=1 30 count=1
20 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile 31 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
21 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
22 for sample in $samples; do 32 for sample in $samples; do
23 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" 33 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
24 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile 34 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
25 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile 35 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
26 36