Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg

comparison r_wrapper.sh @ 7:a9053212a462 draft

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author davidvanzessen
date Mon, 05 Jan 2015 09:30:08 -0500
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children 043fd6613fd9
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6:8b46fca04595 7:a9053212a462
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 filterproductive=$7
10 useD="false"
11 if [[ "$species" == "human" && "$locus" = "igh" ]] ; then
12 useD="true"
13 fi
14 dir="$(cd "$(dirname "$0")" && pwd)"
15 mkdir $3
16 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $filterproductive 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 samples=`cat $outputDir/samples.txt`
22 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)<br />" > $2
23 echo "<table border = 1>" >> $2
24 echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
25 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
26 do
27 echo "<tr><td>$sample</td>" >> $2
28 echo "<td>$all</td>" >> $2
29 echo "<td>$productive (${perc_prod}%)</td>" >> $2
30 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2
31 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2
32 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2
33 done < $outputDir/productive_counting.txt
34 echo "</table border></center></html>" >> $2
35
36 echo "productive_counting.txt"
37 echo "<html><head><title>Report on:" >> $outputFile
38 for sample in $samples; do
39 echo " $sample" >> $outputFile
40 done
41 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
42 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
43 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
44 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
45 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
46
47 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
48 echo "<img src='VFPlot.png'/>" >> $outputFile
49 if [[ "$useD" == "true" ]] ; then
50 echo "<img src='DFPlot.png'/>" >> $outputFile
51 fi
52 echo "<img src='JFPlot.png'/>" >> $outputFile
53 echo "<img src='VPlot.png'/>" >> $outputFile
54 if [[ "$useD" == "true" ]] ; then
55 echo "<img src='DPlot.png'/>" >> $outputFile
56 fi
57 echo "<img src='JPlot.png'/></div>" >> $outputFile
58
59 count=1
60 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
61 for sample in $samples; do
62 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
63 if [[ "$useD" == "true" ]] ; then
64 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile
65 fi
66 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile
67 if [[ "$useD" == "true" ]] ; then
68 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile
69 fi
70 echo "</tr></table></div>" >> $outputFile
71 count=$((count+1))
72 done
73 echo "</div></div>" >> $outputFile
74
75 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
76
77 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
78 echo "$hasReplicateColumn"
79 #if its a 'new' merged file with replicate info
80 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
81 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
82 for sample in $samples; do
83 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
84 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
85 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
86
87 #replicate,reads,squared
88 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
89 while IFS=, read replicate reads squared
90 do
91
92 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
93 done < $outputDir/ReplicateReads_$sample.csv
94
95 #sum of reads and reads squared
96 while IFS=, read readsSum squaredSum
97 do
98 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
99 done < $outputDir/ReplicateSumReads_$sample.csv
100
101 #overview
102 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
103 while IFS=, read type count weight weightedCount
104 do
105 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
106 done < $outputDir/ClonalityOverView_$sample.csv
107 echo "</table></div>" >> $outputFile
108 done
109 echo "</div></div>" >> $outputFile
110 fi
111
112 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
113
114 if [[ "$hasJunctionData" == "Yes" ]] ; then
115 echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'><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>" >> $outputFile
116 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
117 do
118 echo "<tr><td>$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
119 done < $outputDir/junctionAnalysis.csv
120 echo "</tbody></table></div>" >> $outputFile
121 fi
122
123 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
124 for sample in $samples; do
125 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
126 done
127 echo "</table><div name='comparisonarea'>" >> $outputFile
128 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
129 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
130 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
131 echo "</div></div>" >> $outputFile
132
133 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
134 echo "<table border='1'>" >> $outputFile
135 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
136 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
137 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
138
139 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
140
141 echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
142 if [[ "$useD" == "true" ]] ; then
143 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
144 fi
145 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
146
147 echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
148 if [[ "$useD" == "true" ]] ; then
149 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
150 fi
151 echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
152
153 for sample in $samples; do
154 if [[ "$useD" == "true" ]] ; then
155 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
156 fi
157 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
158 if [[ "$useD" == "true" ]] ; then
159 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
160 fi
161 done
162
163 echo "</table>" >> $outputFile
164 echo "</div></html>" >> $outputFile