Mercurial > repos > davidvanzessen > imgt_immunerepertoire_igg

comparison combined.sh @ 3:8b026af4b298 draft default tip

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author davidvanzessen
date Tue, 11 Mar 2014 10:39:04 -0400
parents 3cce6e04b1e8
children
comparison
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2:84a386d96452 3:8b026af4b298
42 echo "<tr><td>-----------------------------------</td></tr>" >> $html 42 echo "<tr><td>-----------------------------------</td></tr>" >> $html
43 echo "<tr><td>plotting</td></tr>" >> $html 43 echo "<tr><td>plotting</td></tr>" >> $html
44 44
45 45
46 inputFile=$PWD/merged.txt 46 inputFile=$PWD/merged.txt
47 outputFile=$html
48 outputDir=$imageDir 47 outputDir=$imageDir
48 outputFile=$outputDir/index.html
49 mkdir $outputDir 49 mkdir $outputDir
50 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1 50 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
51 echo "<html>" > $outputFile 51 cp $dir/tabber.js $outputDir
52 cp $dir/style.css $outputDir
53 cp $dir/script.js $outputDir
54 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)</center></html>" > $html
55 echo "<html><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'><div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
52 echo "<img src='VPlot.png'/>" >> $outputFile 56 echo "<img src='VPlot.png'/>" >> $outputFile
53 echo "<img src='DPlot.png'/>" >> $outputFile 57 echo "<img src='DPlot.png'/>" >> $outputFile
54 echo "<img src='JPlot.png'/>" >> $outputFile 58 echo "<img src='JPlot.png'/></div>" >> $outputFile
55 59
56 samples=`cat $outputDir/samples.txt` 60 samples=`cat $outputDir/samples.txt`
57 count=1 61 count=1
58 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile 62 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
63 for sample in $samples; do
64 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
65
66 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
67 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
68 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
69 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
70 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
71 echo "<td><img src='DJ_$sample.png'/></td></tr></table></div>" >> $outputFile
72 count=$((count+1))
73 done
74 echo "</div></div>" >> $outputFile
75
76
59 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" 77 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
60 for sample in $samples; do 78 echo "$hasReplicateColumn"
61 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" 79 #if its a 'new' merged file with replicate info
62 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile 80 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
63 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile 81 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
64 82 for sample in $samples; do
65 echo "$hasReplicateColumn" 83 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
66 #if its a 'new' merged file with replicate info 84 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
67 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 85 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
68 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
69 86
70 #replicate,reads,squared 87 #replicate,reads,squared
71 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile 88 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
72 while IFS=, read replicate reads squared 89 while IFS=, read replicate reads squared
73 do 90 do
74 91
75 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile 92 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
76 done < $outputDir/ReplicateReads_$sample.csv 93 done < $outputDir/ReplicateReads_$sample.csv
77 94
78 #sum of reads and reads squared 95 #sum of reads and reads squared
79 while IFS=, read readsSum squaredSum 96 while IFS=, read readsSum squaredSum
80 do 97 do
81 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile 98 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
82 done < $outputDir/ReplicateSumReads_$sample.csv 99 done < $outputDir/ReplicateSumReads_$sample.csv
83 100
84 echo "</table></td></tr>" >> $outputFile
85
86 #overview 101 #overview
87 echo "<tr><td colspan='3'><table border='1'><tr><th>Coincidence Type</th><th>Raw Coincidence Freq</th><th>Coincidence Weight</th><th>Coincidences, Weighted</th></tr>" >> $outputFile 102 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
88 while IFS=, read type count weight weightedCount 103 while IFS=, read type count weight weightedCount
89 do 104 do
90 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile 105 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
91 done < $outputDir/ClonalityOverView_$sample.csv 106 done < $outputDir/ClonalityOverView_$sample.csv
92 echo "</table></td></tr>" >> $outputFile 107 echo "</table></div>" >> $outputFile
93 fi 108 done
109 echo "</div></div>" >> $outputFile
110 fi
94 111
95 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>" >> $outputFile 112 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
96 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" 113 echo "<div class='tabbertab' title='Junction Analysis'><table border='1'><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th></tr>" >> $outputFile
97 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile 114 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
98 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" 115 do
99 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile 116 echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
100 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" 117 done < $outputDir/junctionAnalysis.csv
101 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile 118 echo "</table></div>" >> $outputFile
102 count=$((count+1)) 119 fi
120
121 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
122 for sample in $samples; do
123 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
103 done 124 done
125 echo "</table><div name='comparisonarea'>" >> $outputFile
126 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
127 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
128 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
129 echo "</div></div>" >> $outputFile
130
131 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
132 echo "<table border='1'>" >> $outputFile
133 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
134 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.tsv'>Download</a></td></tr>" >> $outputFile
135 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.tsv'>Download</a></td></tr>" >> $outputFile
104 echo "</table>" >> $outputFile 136 echo "</table>" >> $outputFile
105 137 echo "</div>" >> $outputFile
106 echo "</html>" >> $outputFile