Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison wrapper.sh @ 0:c5ac9a871b26 draft

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author davidvanzessen
date Thu, 19 Jun 2014 10:39:41 -0400
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children c0110597898e
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-1:000000000000 0:c5ac9a871b26
1 #!/bin/bash
2
3 inputFile=$1
4 outputFile=$2
5 outputDir=$3
6
7 dir="$(cd "$(dirname "$0")" && pwd)"
8 mkdir $outputDir
9
10 Rscript --verbose $dir/RScript.r $inputFile $outputDir 2>&1
11 cp $dir/jquery-1.11.0.min.js $outputDir
12 cp $dir/script.js $outputDir
13 cp $dir/style.css $outputDir
14 cp $dir/tabber.js $outputDir
15
16 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>" > $outputFile
17
18 cd $outputDir
19
20 html="index.html"
21 echo "<html><head><title>Result</title>" > $html
22 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $html
23 echo "<script type='text/javascript' src='tabber.js'></script>" >> $html
24 echo "<script type='text/javascript' src='script.js'></script>" >> $html
25 echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $html
26 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $html
27 echo "<div id='hidden_div' style='display: none;'></div>" >> $html
28 echo "<div class='tabber'>" >> $html
29 while read patient sample1 sample2
30 do
31 echo "$patient"
32 oldLocus=""
33 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
34 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
35 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
36 echo "<div class='tabbertab' title='$patient'>" >> $html
37 echo "<div class='tabber'>" >> $html
38 echo "<div class='tabbertab' title='Data frequency'>" >> $html
39 echo "<table><tr><td style='vertical-align:top;'>" >> $html
40 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html
41 echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
42 echo "<tbody>" >> $html
43 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent
44 do
45 if [ "$locus" != "$oldLocus" ] ; then
46 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
47 echo "<tr><td><b>$locus</b></td>" >> $html
48 else
49 echo "<td></td>" >> $html
50 fi
51 echo "<td>$v_segment</td>" >> $html
52 echo "<td>$j_segment</td>" >> $html
53 echo "<td>>$cut_off_value</td>" >> $html
54 if [ "$both" != "0" ] ; then
55 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$both</td>" >> $html
56 else
57 echo "<td>$both</td>" >> $html
58 fi
59 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
60 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> $html
61 else
62 echo "<td>$one</td>" >> $html
63 fi
64 echo "<td>$read_count1</td>" >> $html
65 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
66 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> $html
67 else
68 echo "<td>$two</td>" >> $html
69 fi
70 echo "<td>$read_count2</td>" >> $html
71 echo "<td>$sum</td>" >> $html
72 echo "<td>${percent}&#37;</td>" >> $html
73 echo "</tr>" >> $html
74 oldLocus="$locus"
75 done < tmp.txt
76 echo "</tbody></table>" >> $html
77 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table></div>" >> $html
78 echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
79 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> $html
80 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> $html
81 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> $html
82
83 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
84 echo "<div class='tabbertab' title='Data reads'>" >> $html
85 echo "<table><tr><td style='vertical-align:top;'>" >> $html
86 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html
87 echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
88 echo "<tbody>" >> $html
89 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent
90 do
91 if [ "$locus" != "$oldLocus" ] ; then
92 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
93 echo "<tr><td><b>$locus</b></td>" >> $html
94 else
95 echo "<td></td>" >> $html
96 fi
97 echo "<td>$v_segment</td>" >> $html
98 echo "<td>$j_segment</td>" >> $html
99 echo "<td>>$cut_off_value</td>" >> $html
100 if [ "$both" != "0" ] ; then
101 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$both</td>" >> $html
102 else
103 echo "<td>$both</td>" >> $html
104 fi
105 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
106 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> $html
107 else
108 echo "<td>$one</td>" >> $html
109 fi
110 echo "<td>$read_count1</td>" >> $html
111 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
112 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> $html
113 else
114 echo "<td>$two</td>" >> $html
115 fi
116 echo "<td>$read_count2</td>" >> $html
117 echo "<td>$sum</td>" >> $html
118 echo "<td>${percent}&#37;</td>" >> $html
119 echo "</tr>" >> $html
120 oldLocus="$locus"
121 done < tmp.txt
122 echo "</tbody></table>" >> $html
123 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table></div>" >> $html
124 echo "<div class='tabbertab' title='Graphs reads'>" >> $html
125 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
126 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> $html
127 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> $html
128 echo "</div>" >> $html
129 echo "</div>" >> $html
130 done < patients.txt
131 echo "</div></html>" >> $html
132 rm tmp.txt