Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg

comparison r_wrapper_b.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=$7
10
11 useD="false"
12 if [[ "$species" == "human" && "$locus" = "igh" ]] ; then
13 useD="true"
14 fi
15 dir="$(cd "$(dirname "$0")" && pwd)"
16 mkdir $3
17 Rscript --verbose $dir/RScript_b.r $inputFile $outputDir $outputDir $clonalType $species $locus $selection 2>&1
18 cp $dir/tabber.js $outputDir
19 cp $dir/style.css $outputDir
20 cp $dir/script.js $outputDir
21 cp $dir/jquery-1.11.0.min.js $outputDir
22 cp $dir/jquery.tablesorter.min.js $outputDir
23 cp $dir/asc.gif $outputDir
24 cp $dir/desc.gif $outputDir
25 cp $dir/bg.gif $outputDir
26 samples=`cat $outputDir/samples.txt`
27 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
28 echo "<html><head><title>Report on:" >> $outputFile
29 for sample in $samples; do
30 echo " $sample" >> $outputFile
31 done
32 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
33 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
34 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
35 echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile
36 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
37 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
38
39 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
40 echo "<img src='VFPlot.png'/>" >> $outputFile
41 if [[ "$useD" == "true" ]] ; then
42 echo "<img src='DFPlot.png'/>" >> $outputFile
43 fi
44 echo "<img src='JFPlot.png'/>" >> $outputFile
45 echo "<img src='VPlot.png'/>" >> $outputFile
46 if [[ "$useD" == "true" ]] ; then
47 echo "<img src='DPlot.png'/>" >> $outputFile
48 fi
49 echo "<img src='JPlot.png'/></div>" >> $outputFile
50
51 count=1
52 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
53 for sample in $samples; do
54 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
55 if [[ "$useD" == "true" ]] ; then
56 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile
57 fi
58 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile
59 if [[ "$useD" == "true" ]] ; then
60 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile
61 fi
62 echo "</tr></table></div>" >> $outputFile
63 count=$((count+1))
64 done
65 echo "</div></div>" >> $outputFile
66
67 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
68
69 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
70 echo "$hasReplicateColumn"
71 #if its a 'new' merged file with replicate info
72 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
73 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
74 for sample in $samples; do
75 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
76 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
77 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
78
79 #replicate,reads,squared
80 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
81 while IFS=, read replicate reads squared
82 do
83
84 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
85 done < $outputDir/ReplicateReads_$sample.csv
86
87 #sum of reads and reads squared
88 while IFS=, read readsSum squaredSum
89 do
90 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
91 done < $outputDir/ReplicateSumReads_$sample.csv
92
93 #overview
94 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
95 while IFS=, read type count weight weightedCount
96 do
97 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
98 done < $outputDir/ClonalityOverView_$sample.csv
99 echo "</table></div>" >> $outputFile
100 done
101 echo "</div></div>" >> $outputFile
102 fi
103
104 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
105
106 if [[ "$hasJunctionData" == "Yes" ]] ; then
107 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>" >> $outputFile
108 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
109 do
110 echo "<tr><td>$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
111 done < $outputDir/junctionAnalysis.csv
112 echo "</tbody></table></div>" >> $outputFile
113 fi
114
115 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
116 for sample in $samples; do
117 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
118 done
119 echo "</table><div name='comparisonarea'>" >> $outputFile
120 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
121 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
122 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
123 echo "</div></div>" >> $outputFile
124
125 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
126 echo "<table border='1'>" >> $outputFile
127 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
128 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
129 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
130
131 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
132
133 echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
134 if [[ "$useD" == "true" ]] ; then
135 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
136 fi
137 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
138
139 echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
140 if [[ "$useD" == "true" ]] ; then
141 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
142 fi
143 echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
144
145 for sample in $samples; do
146 if [[ "$useD" == "true" ]] ; then
147 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
148 fi
149 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
150 if [[ "$useD" == "true" ]] ; then
151 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
152 fi
153 done
154
155 echo "</table>" >> $outputFile
156 echo "</div></html>" >> $outputFile