Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg

comparison r_wrapper_t.sh @ 1:778a9d130904 draft

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author davidvanzessen
date Thu, 04 Sep 2014 07:46:23 -0400
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0:7d97fa9a0423 1:778a9d130904
1 #!/bin/bash
2
3 inputFile=$1
4 outputDir=$3
5 outputFile=$3/index.html #$2
6 clonalType=$4
7 species=$5
8 locus=$6
9 selection=$7
10 useD="true"
11 if [[ "$species" == "human" && "$locus" = "tra" ]] ; then
12 useD="false"
13 fi
14 dir="$(cd "$(dirname "$0")" && pwd)"
15 mkdir $3
16 Rscript --verbose $dir/RScript_t.r $inputFile $outputDir $outputDir $clonalType $species $locus $selection 2>&1
17 cp $dir/tabber.js $outputDir
18 cp $dir/style.css $outputDir
19 cp $dir/script.js $outputDir
20 cp $dir/jquery-1.11.0.min.js $outputDir
21 cp $dir/jquery.tablesorter.min.js $outputDir
22 cp $dir/asc.gif $outputDir
23 cp $dir/desc.gif $outputDir
24 cp $dir/bg.gif $outputDir
25 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>" > $2
26 echo "<html<head>" >> $outputFile
27 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
28 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
29 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
30 echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile
31 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
32 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
33
34 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
35 echo "<img src='VFPlot.png'/>" >> $outputFile
36 if [[ "$useD" == "true" ]] ; then
37 echo "<img src='DFPlot.png'/>" >> $outputFile
38 fi
39 echo "<img src='JFPlot.png'/>" >> $outputFile
40 echo "<img src='VPlot.png'/>" >> $outputFile
41 if [[ "$useD" == "true" ]] ; then
42 echo "<img src='DPlot.png'/>" >> $outputFile
43 fi
44 echo "<img src='JPlot.png'/></div>" >> $outputFile
45
46 samples=`cat $outputDir/samples.txt`
47 count=1
48 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
49 for sample in $samples; do
50 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
51 if [[ "$useD" == "true" ]] ; then
52 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile
53 fi
54 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile
55 if [[ "$useD" == "true" ]] ; then
56 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile
57 fi
58 echo "</tr></table></div>" >> $outputFile
59 count=$((count+1))
60 done
61 echo "</div></div>" >> $outputFile
62
63
64 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
65 echo "$hasReplicateColumn"
66 #if its a 'new' merged file with replicate info
67 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
68 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
69 for sample in $samples; do
70 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
71 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
72 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
73
74 #replicate,reads,squared
75 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
76 while IFS=, read replicate reads squared
77 do
78
79 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
80 done < $outputDir/ReplicateReads_$sample.csv
81
82 #sum of reads and reads squared
83 while IFS=, read readsSum squaredSum
84 do
85 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
86 done < $outputDir/ReplicateSumReads_$sample.csv
87
88 #overview
89 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
90 while IFS=, read type count weight weightedCount
91 do
92 echo "<tr><td><a href='ClonalitySequences_${sample}_${type}.csv'>$type</a></td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
93 done < $outputDir/ClonalityOverView_$sample.csv
94 echo "</table></div>" >> $outputFile
95 done
96 echo "</div></div>" >> $outputFile
97 fi
98
99 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
100
101 if [[ "$hasJunctionData" == "Yes" ]] ; then
102 echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table' class='tablesorter'><thead><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><thead></tr><tbody>" >> $outputFile
103 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
104 do
105 echo "<tr><td>$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
106 done < $outputDir/junctionAnalysis.csv
107 echo "</tbody></table></div>" >> $outputFile
108 fi
109
110 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
111 for sample in $samples; do
112 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
113 done
114 echo "</table><div name='comparisonarea'>" >> $outputFile
115 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
116 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
117 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
118 echo "</div></div>" >> $outputFile
119
120 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
121 echo "<table border='1'>" >> $outputFile
122 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
123 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile
124 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile
125
126 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
127
128 echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
129 if [[ "$useD" == "true" ]] ; then
130 echo "<tr><td>The dataset used to generate the D gene family frequency graph</td><td><a href='DFFrequency.csv'>Download</a></td></tr>" >> $outputFile
131 fi
132 echo "<tr><td>The dataset used to generate the J gene family frequency graph</td><td><a href='JFFrequency.csv'>Download</a></td></tr>" >> $outputFile
133
134 echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
135 if [[ "$useD" == "true" ]] ; then
136 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
137 fi
138 echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
139
140 for sample in $samples; do
141 if [[ "$useD" == "true" ]] ; then
142 echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.csv'>Download</a></td></tr>" >> $outputFile
143 fi
144 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
145 if [[ "$useD" == "true" ]] ; then
146 echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
147 fi
148 done
149
150 echo "</table>" >> $outputFile
151 echo "</div></html>" >> $outputFile