annotate report_clonality/r_wrapper.sh @ 9:efa1f5a17b6e draft

Uploaded
author davidvanzessen
date Mon, 19 Dec 2016 09:23:01 -0500
parents 8cbc1a8d27ae
children 5f5d29c5e711
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
1 #!/bin/bash
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
3 inputFile=$1
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
4 outputDir=$3
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
5 outputFile=$3/index.html #$2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
6 clonalType=$4
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
7 species=$5
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
8 locus=$6
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
9 filterproductive=$7
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
10 clonality_method=$8
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
11
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
12 dir="$(cd "$(dirname "$0")" && pwd)"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
13 useD="false"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
14 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
15 echo "species D region in reference db"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
16 useD="true"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
17 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
18 echo "$species"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
19 if [[ "$species" == *"custom"* ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
20 loci=(${locus//;/ })
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
21 useD="true"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
22 echo "${loci[@]}"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
23 if [[ "${#loci[@]}" -eq "2" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
24 useD="false"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
25 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
26 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
27 mkdir $3
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
28 cp $dir/genes.txt $outputDir
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
29 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
30 cp $dir/tabber.js $outputDir
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
31 cp $dir/style.css $outputDir
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
32 cp $dir/script.js $outputDir
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
33 cp $dir/jquery-1.11.0.min.js $outputDir
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
34 cp $dir/pure-min.css $outputDir
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
35 samples=`cat $outputDir/samples.txt`
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
36
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
37 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
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
38 echo "<table border = 1>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
39 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>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
40 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
41 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
42 echo "<tr><td>$sample</td>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
43 echo "<td>$all</td>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
44 echo "<td>$productive (${perc_prod}%)</td>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
45 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
46 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
47 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
48 done < $outputDir/productive_counting.txt
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
49 echo "</table border></center></html>" >> $2
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
50
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
51 echo "<html><head><title>Report on:" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
52
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
53 mkdir $outputDir/circos
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
54 cp $dir/circos/* $outputDir/circos/
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
55 #CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
56 #CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
57
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
58 #CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
59 #CIRCOSDIR="/home/galaxy/Anaconda3/bin"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
60
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
61 USECIRCOS="no"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
62 if [ -d "$CIRCOSDIR" ]; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
63 USECIRCOS="yes"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
64 else
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
65 if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
66 USECIRCOS="yes"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
67 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
68 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
69 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
70 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
71 echo "Using Circos: $USECIRCOS"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
72 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
73 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
74 echo " $sample" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
75
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
76 if [[ "$USECIRCOS" != "yes" ]]; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
77 continue
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
78 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
79
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
80 circos_file="$outputDir/${sample}_VJ_circos.txt"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
81 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
82 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
83 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
84 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
85
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
86
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
87 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
88 circos_file="$outputDir/${sample}_VD_circos.txt"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
89 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
90 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
91 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
92 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
93
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
94 circos_file="$outputDir/${sample}_DJ_circos.txt"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
95 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
96 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
97 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
98 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
99
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
100 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
101 done
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
102 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
103 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
104 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
105 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
106 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
107 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
108
8
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
109
5
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
110 echo "<img src='VFPlot.png'/>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
111 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
112 echo "<img src='DFPlot.png'/>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
113 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
114 echo "<img src='VPlot.png'/>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
115 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
116 echo "<img src='DPlot.png'/>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
117 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
118 echo "<img src='JPlot.png'/>" >> $outputFile
8
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
119 echo "</div>" >> $outputFile
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
120
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
121 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
122 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
5
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
123 echo "<img src='AAComposition.png'/>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
124 echo "<img src='DReadingFrame.png'/>" >> $outputFile
8
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
125
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
126 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
127 echo "<thead><tr><th>Sample</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
128 while IFS=, read Sample median
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
129 do
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
130 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
131 done < $outputDir/AAMedianBySample.csv
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
132 echo "</table>" >> $outputFile
8cbc1a8d27ae Uploaded
davidvanzessen
parents: 5
diff changeset
133
5
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
134 echo "</div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
135
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
136 #Heatmaps
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
137
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
138 count=1
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
139 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
140 for sample in $samples; do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
141 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
142 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
143 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
144 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
145 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
146 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
147 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
148 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
149 echo "</tr></table></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
150 count=$((count+1))
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
151 done
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
152 echo "</div></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
153
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
154 #circos
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
155
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
156 if [[ "$USECIRCOS" == "yes" ]]; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
157
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
158 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
159 for sample in $samples; do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
160 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
161 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
162 echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
163 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
164 echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
165 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
166 echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
167 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
168 echo "<center></table></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
169 count=$((count+1))
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
170 done
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
171 echo "</div></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
172 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
173 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
174
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
175 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
176 echo "$hasReplicateColumn"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
177 #if its a 'new' merged file with replicate info
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
178 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
179 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
180 for sample in $samples; do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
181 echo "${clonality_method}"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
182 if [[ "${clonality_method}" == "old" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
183 echo "in old"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
184 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
185 echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
186 echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
187
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
188 #replicate,reads,squared
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
189 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
190 while IFS=, read replicate reads squared
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
191 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
192 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
193 done < $outputDir/ReplicateReads_$sample.csv
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
194
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
195 #sum of reads and reads squared
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
196 while IFS=, read readsSum squaredSum
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
197 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
198 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
199 done < $outputDir/ReplicateSumReads_$sample.csv
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
200
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
201 #overview
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
202 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
203 while IFS=, read type count weight weightedCount
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
204 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
205 if [[ "$type" -eq "1" ]]; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
206 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
207 else
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
208 echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
209 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
210
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
211 done < $outputDir/ClonalityOverView_$sample.csv
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
212 echo "</table></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
213 else
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
214 echo "in new"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
215 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
216 echo "<div class='tabbertab' title='$sample'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
217 echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
218 echo "<table border = 1>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
219 while IFS=, read type count
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
220 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
221 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
222 done < $outputDir/lymphclon_coincidences_$sample.csv
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
223 echo "</table></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
224 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
225 done
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
226 echo "</div></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
227 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
228
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
229 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
230
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
231 #if [[ "$hasJunctionData" == "Yes" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
232 if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
233 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
234 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
235 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
236 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
237 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
238 done < $outputDir/junctionAnalysisProd_mean.csv
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
239 echo "</tbody></table>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
240
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
241 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
242 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
243 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
244 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
245 done < $outputDir/junctionAnalysisUnProd_mean.csv
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
246 echo "</tbody></table>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
247
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
248 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
249 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
250 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
251 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
252 done < $outputDir/junctionAnalysisProd_median.csv
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
253 echo "</tbody></table>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
254
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
255 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
256 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
257 do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
258 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
259 done < $outputDir/junctionAnalysisUnProd_median.csv
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
260 echo "</tbody></table>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
261
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
262 echo "</div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
263 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
264
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
265 echo "<div class='tabbertab' title='Comparison'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
266 for sample in $samples; do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
267 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
268 done
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
269 echo "</table><div name='comparisonarea'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
270 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
271 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
272 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
273 echo "</div></div>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
274
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
275 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
276 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
277 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
278 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
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
279 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
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
280
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
281 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
282
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
283 echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
284 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
285 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
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
286 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
287
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
288 echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
289 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
290 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
291 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
292 echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
293 echo "<tr><td>The dataset used to generate the AA composition graph</td><td><a href='AAComposition.csv'>Download</a></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
294
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
295 for sample in $samples; do
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
296 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
297 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
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
298 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
299 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
300 if [[ "$useD" == "true" ]] ; then
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
301 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
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
302 fi
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
303 done
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
304
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
305 echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
306
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
307 echo "</table>" >> $outputFile
bcec7bb4e089 Uploaded
davidvanzessen
parents:
diff changeset
308 echo "</div></html>" >> $outputFile