Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison wrapper.sh @ 29:5ab17bdf2530 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Fri, 22 May 2015 09:06:04 -0400
parents 0940835d259c
children 45554fd15511
comparison
equal deleted inserted replaced
28:a63ccc36f5a4 29:5ab17bdf2530
3 inputFile=$1 3 inputFile=$1
4 outputFile=$2 4 outputFile=$2
5 outputDir=$3 5 outputDir=$3
6 min_freq=$4 6 min_freq=$4
7 min_cells=$5 7 min_cells=$5
8 merge_on="$6"
8 9
9 dir="$(cd "$(dirname "$0")" && pwd)" 10 dir="$(cd "$(dirname "$0")" && pwd)"
10 mkdir $outputDir 11 mkdir $outputDir
11 12
12 13
13 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells 2>&1 14 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells "${merge_on}" 2>&1
14 cp $dir/jquery-1.11.0.min.js $outputDir 15 cp $dir/jquery-1.11.0.min.js $outputDir
15 cp $dir/script.js $outputDir 16 cp $dir/script.js $outputDir
16 cp $dir/style.css $outputDir 17 cp $dir/style.css $outputDir
17 cp $dir/tabber.js $outputDir 18 cp $dir/tabber.js $outputDir
18 19
49 echo "<div class='tabbertab' title='Data frequency'>" >> "$html" 50 echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
50 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" 51 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
51 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html" 52 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
52 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" 53 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"
53 echo "<tbody>" >> "$html" 54 echo "<tbody>" >> "$html"
55 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>"
54 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 56 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
55 do 57 do
56 if [ "$locus" != "$oldLocus" ] ; then 58 if [ "$locus" != "$oldLocus" ] ; then
57 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>" >> "$html" 59 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
58 echo "<tr><td><b>$locus</b></td>" >> "$html" 60 echo "<tr><td><b>$locus</b></td>" >> "$html"
80 fi 82 fi
81 echo "<td>$read_count2</td>" >> "$html" 83 echo "<td>$read_count2</td>" >> "$html"
82 echo "<td>$sum</td>" >> "$html" 84 echo "<td>$sum</td>" >> "$html"
83 echo "<td>${percent}&#37;</td>" >> "$html" 85 echo "<td>${percent}&#37;</td>" >> "$html"
84 echo "</tr>" >> "$html" 86 echo "</tr>" >> "$html"
85 oldLocus="$locus" 87 oldLocus="$locus"
88 if [ "${cut_off_value}" == "0" ] ; then
89 scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /><br />"
90 fi
86 done < tmp.txt 91 done < tmp.txt
87 echo "</tbody></table>" >> "$html" 92 echo "</tbody></table>" >> "$html"
88 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html" 93 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
89 echo "</div>" >> "$html" 94 echo "</div>" >> "$html"
90 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html" 95 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
91 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html" 96 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html"
92 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html" 97 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html"
93 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html" 98 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
99 echo "${scatterplot_tab}</div>" >> "$html"
94 100
95 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt 101 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
96 echo "<div class='tabbertab' title='Data reads'>" >> "$html" 102 echo "<div class='tabbertab' title='Data reads'>" >> "$html"
97 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" 103 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
98 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html" 104 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
99 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" 105 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"
100 echo "<tbody>" >> "$html" 106 echo "<tbody>" >> "$html"
107 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>"
101 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 108 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
102 do 109 do
103 if [ "$locus" != "$oldLocus" ] ; then 110 if [ "$locus" != "$oldLocus" ] ; then
104 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>" >> "$html" 111 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
105 echo "<tr><td><b>$locus</b></td>" >> "$html" 112 echo "<tr><td><b>$locus</b></td>" >> "$html"
128 echo "<td>$read_count2</td>" >> "$html" 135 echo "<td>$read_count2</td>" >> "$html"
129 echo "<td>$sum</td>" >> "$html" 136 echo "<td>$sum</td>" >> "$html"
130 echo "<td>${percent}&#37;</td>" >> "$html" 137 echo "<td>${percent}&#37;</td>" >> "$html"
131 echo "</tr>" >> "$html" 138 echo "</tr>" >> "$html"
132 oldLocus="$locus" 139 oldLocus="$locus"
140 if [ "${cut_off_value}" == "0" ] ; then
141 scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /><br />"
142 fi
133 done < tmp.txt 143 done < tmp.txt
134 echo "</tbody></table>" >> "$html" 144 echo "</tbody></table>" >> "$html"
135 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html" 145 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
136 echo "</div>" >> "$html" 146 echo "</div>" >> "$html"
137 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html" 147 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
138 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html" 148 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html"
139 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html" 149 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html"
140 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html" 150 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html"
151 echo "${scatterplot_tab}</div>" >> "$html"
141 echo "</div>" >> "$html" 152 echo "</div>" >> "$html"
142 echo "</div>" >> "$html" 153 echo "</div>" >> "$html"
143 echo "</html>" >> "$html" 154 echo "</html>" >> "$html"
144 done < patients.txt 155 done < patients.txt
145 156
146 html="index.html" 157 html="index.html"
147 echo "<html>" > $html 158 echo "<html>" > $html
148 echo "<table>" >> "$html" 159 echo "<table>" >> "$html"
149 echo "<tr><td><b>Singles:</b></td></tr>" >> "$html" 160 echo "<tr><td><b>Singles (<a href='singles_freq_scatterplot.png'>Frequency scatterplot</a>, <a href='singles_reads_scatterplot.png'>Reads scatterplot</a>):</b></td></tr>" >> "$html"
150 for patient in "${singles[@]}" 161 for patient in "${singles[@]}"
151 do 162 do
152 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html" 163 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
153 done 164 done
154 echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> "$html" 165 echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> "$html"