Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison wrapper.sh @ 9:58a28427930e draft

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author davidvanzessen
date Tue, 30 Sep 2014 10:06:57 -0400
parents fa240d1c57a9
children d980e2493657
comparison
equal deleted inserted replaced
8:fa240d1c57a9 9:58a28427930e
27 pairs_R_Dx=() 27 pairs_R_Dx=()
28 while read patient sample1 sample2 type 28 while read patient sample1 sample2 type
29 do 29 do
30 echo "$patient" 30 echo "$patient"
31 html="${patient}.html" 31 html="${patient}.html"
32 echo "$header" > $html 32 echo "$header" > "$html"
33 if [[ "$type" == *pair* ]] ; then 33 if [[ "$type" == *pair* ]] ; then
34 if [[ "$sample1" == *_BM* ]] || [[ "$sample1" == *_PB* ]] ; then 34 if [[ "$sample1" == *_BM* ]] || [[ "$sample1" == *_PB* ]] ; then
35 pairs_BM_PB+=( "$patient" ) 35 pairs_BM_PB+=( "$patient" )
36 elif [[ "$sample1" == *_Left* ]] || [[ "$sample1" == *_Right* ]] ; then 36 elif [[ "$sample1" == *_Left* ]] || [[ "$sample1" == *_Right* ]] ; then
37 pairs_Left_Right+=( "$patient" ) 37 pairs_Left_Right+=( "$patient" )
43 fi 43 fi
44 oldLocus="" 44 oldLocus=""
45 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')" 45 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
46 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')" 46 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
47 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt 47 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
48 echo "<div class='tabber'>" >> $html 48 echo "<div class='tabber'>" >> "$html"
49 echo "<div class='tabbertab' title='Data frequency'>" >> $html 49 echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
50 echo "<table><tr><td style='vertical-align:top;'>" >> $html 50 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
51 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html 51 echo "<table border = 1 class='result_table summary_table' id='summary_table_${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 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 "<tbody>" >> $html 53 echo "<tbody>" >> "$html"
54 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 54 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
55 do 55 do
56 if [ "$locus" != "$oldLocus" ] ; then 56 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>" >> $html 57 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
58 echo "<tr><td><b>$locus</b></td>" >> $html 58 echo "<tr><td><b>$locus</b></td>" >> "$html"
59 else 59 else
60 echo "<td></td>" >> $html 60 echo "<td></td>" >> "$html"
61 fi 61 fi
62 echo "<td>$v_segment</td>" >> $html 62 echo "<td>$v_segment</td>" >> "$html"
63 echo "<td>$j_segment</td>" >> $html 63 echo "<td>$j_segment</td>" >> "$html"
64 echo "<td>>$cut_off_value</td>" >> $html 64 echo "<td>>$cut_off_value</td>" >> "$html"
65 if [ "$both" != "0" ] ; then 65 if [ "$both" != "0" ] ; then
66 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$both</td>" >> $html 66 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$both</td>" >> "$html"
67 else 67 else
68 echo "<td>$both</td>" >> $html 68 echo "<td>$both</td>" >> "$html"
69 fi 69 fi
70 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then 70 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
71 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> $html 71 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html"
72 else 72 else
73 echo "<td>$one</td>" >> $html 73 echo "<td>$one</td>" >> "$html"
74 fi 74 fi
75 echo "<td>$read_count1</td>" >> $html 75 echo "<td>$read_count1</td>" >> "$html"
76 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then 76 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
77 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> $html 77 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html"
78 else 78 else
79 echo "<td>$two</td>" >> $html 79 echo "<td>$two</td>" >> "$html"
80 fi 80 fi
81 echo "<td>$read_count2</td>" >> $html 81 echo "<td>$read_count2</td>" >> "$html"
82 echo "<td>$sum</td>" >> $html 82 echo "<td>$sum</td>" >> "$html"
83 echo "<td>${percent}&#37;</td>" >> $html 83 echo "<td>${percent}&#37;</td>" >> "$html"
84 echo "</tr>" >> $html 84 echo "</tr>" >> "$html"
85 oldLocus="$locus" 85 oldLocus="$locus"
86 done < tmp.txt 86 done < tmp.txt
87 echo "</tbody></table>" >> $html 87 echo "</tbody></table>" >> "$html"
88 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html 88 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
89 echo "</div>" >> $html 89 echo "</div>" >> "$html"
90 echo "<div class='tabbertab' title='Graphs frequency'>" >> $html 90 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
91 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> $html 91 echo "<a href='${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 />" >> $html 92 echo "<a href='${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>" >> $html 93 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
94 94
95 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt 95 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
96 echo "<div class='tabbertab' title='Data reads'>" >> $html 96 echo "<div class='tabbertab' title='Data reads'>" >> "$html"
97 echo "<table><tr><td style='vertical-align:top;'>" >> $html 97 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
98 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html 98 echo "<table border = 1 class='result_table summary_table' id='summary_table_${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 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"
100 echo "<tbody>" >> $html 100 echo "<tbody>" >> "$html"
101 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 101 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
102 do 102 do
103 if [ "$locus" != "$oldLocus" ] ; then 103 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>" >> $html 104 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
105 echo "<tr><td><b>$locus</b></td>" >> $html 105 echo "<tr><td><b>$locus</b></td>" >> "$html"
106 else 106 else
107 echo "<td></td>" >> $html 107 echo "<td></td>" >> "$html"
108 fi 108 fi
109 echo "<td>$v_segment</td>" >> $html 109 echo "<td>$v_segment</td>" >> "$html"
110 echo "<td>$j_segment</td>" >> $html 110 echo "<td>$j_segment</td>" >> "$html"
111 echo "<td>>$cut_off_value</td>" >> $html 111 echo "<td>>$cut_off_value</td>" >> "$html"
112 if [ "$both" != "0" ] ; then 112 if [ "$both" != "0" ] ; then
113 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$both</td>" >> $html 113 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$both</td>" >> "$html"
114 else 114 else
115 echo "<td>$both</td>" >> $html 115 echo "<td>$both</td>" >> "$html"
116 fi 116 fi
117 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then 117 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
118 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> $html 118 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html"
119 else 119 else
120 echo "<td>$one</td>" >> $html 120 echo "<td>$one</td>" >> "$html"
121 fi 121 fi
122 echo "<td>$read_count1</td>" >> $html 122 echo "<td>$read_count1</td>" >> "$html"
123 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then 123 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
124 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> $html 124 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html"
125 else 125 else
126 echo "<td>$two</td>" >> $html 126 echo "<td>$two</td>" >> "$html"
127 fi 127 fi
128 echo "<td>$read_count2</td>" >> $html 128 echo "<td>$read_count2</td>" >> "$html"
129 echo "<td>$sum</td>" >> $html 129 echo "<td>$sum</td>" >> "$html"
130 echo "<td>${percent}&#37;</td>" >> $html 130 echo "<td>${percent}&#37;</td>" >> "$html"
131 echo "</tr>" >> $html 131 echo "</tr>" >> "$html"
132 oldLocus="$locus" 132 oldLocus="$locus"
133 done < tmp.txt 133 done < tmp.txt
134 echo "</tbody></table>" >> $html 134 echo "</tbody></table>" >> "$html"
135 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html 135 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
136 echo "</div>" >> $html 136 echo "</div>" >> "$html"
137 echo "<div class='tabbertab' title='Graphs reads'>" >> $html 137 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
138 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html 138 echo "<a href='${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 />" >> $html 139 echo "<a href='${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>" >> $html 140 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html"
141 echo "</div>" >> $html 141 echo "</div>" >> "$html"
142 echo "</div>" >> $html 142 echo "</div>" >> "$html"
143 echo "</html>" >> $html 143 echo "</html>" >> "$html"
144 done < patients.txt 144 done < patients.txt
145 145
146 html="index.html" 146 html="index.html"
147 echo "<html>" > $html 147 echo "<html>" > $html
148 echo "<table>" >> $html 148 echo "<table>" >> "$html"
149 echo "<tr><td><b>Singles:</b></td></tr>" >> $html 149 echo "<tr><td><b>Singles:</b></td></tr>" >> "$html"
150 for patient in "${singles[@]}" 150 for patient in "${singles[@]}"
151 do 151 do
152 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html 152 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
153 done 153 done
154 echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> $html 154 echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> "$html"
155 for patient in "${pairs_Left_Right[@]}" 155 for patient in "${pairs_Left_Right[@]}"
156 do 156 do
157 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html 157 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
158 done 158 done
159 echo "<tr><td><b>Pairs (BM & PB):</b></td></tr>" >> $html 159 echo "<tr><td><b>Pairs (BM & PB):</b></td></tr>" >> "$html"
160 for patient in "${pairs_BM_PB[@]}" 160 for patient in "${pairs_BM_PB[@]}"
161 do 161 do
162 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html 162 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
163 done 163 done
164 echo "<tr><td><b>Pairs (Dx & R):</b></td></tr>" >> $html 164 echo "<tr><td><b>Pairs (Dx & R):</b></td></tr>" >> "$html"
165 for patient in "${pairs_R_Dx[@]}" 165 for patient in "${pairs_R_Dx[@]}"
166 do 166 do
167 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html 167 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
168 done 168 done
169 echo "<tr><td><b>Triplets:</b></td></tr>" >> $html 169 echo "<tr><td><b>Triplets:</b></td></tr>" >> "$html"
170 170
171 while read sample1 sample2 sample3 171 while read sample1 sample2 sample3
172 do 172 do
173 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')" 173 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
174 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')" 174 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
178 html="${patient}.html" 178 html="${patient}.html"
179 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html" 179 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
180 echo "$header" > $html 180 echo "$header" > $html
181 oldLocus="" 181 oldLocus=""
182 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt 182 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
183 echo "<div class='tabber'>" >> $html 183 echo "<div class='tabber'>" >> "$html"
184 echo "<div class='tabbertab' title='Data frequency'>" >> $html 184 echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
185 echo "<table><tr><td style='vertical-align:top;'>" >> $html 185 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
186 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html 186 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
187 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 ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> $html 187 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 ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> "$html"
188 echo "<tbody>" >> $html 188 echo "<tbody>" >> "$html"
189 while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 189 while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3
190 do 190 do
191 if [ "$locus" != "$oldLocus" ] ; then 191 if [ "$locus" != "$oldLocus" ] ; then
192 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>" >> $html 192 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
193 echo "<tr><td><b>$locus</b></td>" >> $html 193 echo "<tr><td><b>$locus</b></td>" >> "$html"
194 else 194 else
195 echo "<td></td>" >> $html 195 echo "<td></td>" >> "$html"
196 fi 196 fi
197 echo "<td>$v_segment</td>" >> $html 197 echo "<td>$v_segment</td>" >> "$html"
198 echo "<td>$j_segment</td>" >> $html 198 echo "<td>$j_segment</td>" >> "$html"
199 echo "<td>>$cut_off_value</td>" >> $html 199 echo "<td>>$cut_off_value</td>" >> "$html"
200 if [ "$all" != "0" ] ; then 200 if [ "$all" != "0" ] ; then
201 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$all</td>" >> $html 201 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$all</td>" >> "$html"
202 else 202 else
203 echo "<td>$all</td>" >> $html 203 echo "<td>$all</td>" >> "$html"
204 fi 204 fi
205 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then 205 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
206 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> $html 206 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html"
207 else 207 else
208 echo "<td>$one</td>" >> $html 208 echo "<td>$one</td>" >> "$html"
209 fi 209 fi
210 echo "<td>$read_count1</td>" >> $html 210 echo "<td>$read_count1</td>" >> "$html"
211 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then 211 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
212 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> $html 212 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html"
213 else 213 else
214 echo "<td>$two</td>" >> $html 214 echo "<td>$two</td>" >> "$html"
215 fi 215 fi
216 echo "<td>$read_count2</td>" >> $html 216 echo "<td>$read_count2</td>" >> "$html"
217 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then 217 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
218 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> $html 218 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> "$html"
219 else 219 else
220 echo "<td>$three</td>" >> $html 220 echo "<td>$three</td>" >> "$html"
221 fi 221 fi
222 echo "<td>$read_count3</td>" >> $html 222 echo "<td>$read_count3</td>" >> "$html"
223 echo "</tr>" >> $html 223 echo "</tr>" >> "$html"
224 oldLocus="$locus" 224 oldLocus="$locus"
225 done < tmp.txt 225 done < tmp.txt
226 echo "</tbody></table>" >> $html 226 echo "</tbody></table>" >> "$html"
227 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html 227 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
228 echo "</div>" >> $html 228 echo "</div>" >> "$html"
229 echo "<div class='tabbertab' title='Graphs frequency'>" >> $html 229 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
230 echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> $html 230 echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
231 echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> $html 231 echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
232 232
233 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt 233 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
234 echo "<div class='tabbertab' title='Data reads'>" >> $html 234 echo "<div class='tabbertab' title='Data reads'>" >> "$html"
235 echo "<table><tr><td style='vertical-align:top;'>" >> $html 235 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
236 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html 236 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
237 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 ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> $html 237 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 ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> "$html"
238 echo "<tbody>" >> $html 238 echo "<tbody>" >> "$html"
239 while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 239 while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3
240 do 240 do
241 if [ "$locus" != "$oldLocus" ] ; then 241 if [ "$locus" != "$oldLocus" ] ; then
242 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>" >> $html 242 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
243 echo "<tr><td><b>$locus</b></td>" >> $html 243 echo "<tr><td><b>$locus</b></td>" >> "$html"
244 else 244 else
245 echo "<td></td>" >> $html 245 echo "<td></td>" >> "$html"
246 fi 246 fi
247 echo "<td>$v_segment</td>" >> $html 247 echo "<td>$v_segment</td>" >> "$html"
248 echo "<td>$j_segment</td>" >> $html 248 echo "<td>$j_segment</td>" >> "$html"
249 echo "<td>>$cut_off_value</td>" >> $html 249 echo "<td>>$cut_off_value</td>" >> "$html"
250 if [ "$all" != "0" ] ; then 250 if [ "$all" != "0" ] ; then
251 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$all</td>" >> $html 251 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$all</td>" >> "$html"
252 else 252 else
253 echo "<td>$all</td>" >> $html 253 echo "<td>$all</td>" >> "$html"
254 fi 254 fi
255 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then 255 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
256 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> $html 256 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html"
257 else 257 else
258 echo "<td>$one</td>" >> $html 258 echo "<td>$one</td>" >> "$html"
259 fi 259 fi
260 echo "<td>$read_count1</td>" >> $html 260 echo "<td>$read_count1</td>" >> "$html"
261 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then 261 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
262 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> $html 262 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html"
263 else 263 else
264 echo "<td>$two</td>" >> $html 264 echo "<td>$two</td>" >> "$html"
265 fi 265 fi
266 echo "<td>$read_count2</td>" >> $html 266 echo "<td>$read_count2</td>" >> "$html"
267 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then 267 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
268 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> $html 268 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> "$html"
269 else 269 else
270 echo "<td>$three</td>" >> $html 270 echo "<td>$three</td>" >> "$html"
271 fi 271 fi
272 echo "<td>$read_count3</td>" >> $html 272 echo "<td>$read_count3</td>" >> "$html"
273 echo "</tr>" >> $html 273 echo "</tr>" >> "$html"
274 oldLocus="$locus" 274 oldLocus="$locus"
275 done < tmp.txt 275 done < tmp.txt
276 echo "</tbody></table>" >> $html 276 echo "</tbody></table>" >> "$html"
277 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html 277 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
278 echo "</div>" >> $html 278 echo "</div>" >> "$html"
279 echo "<div class='tabbertab' title='Graphs reads'>" >> $html 279 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
280 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> $html 280 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
281 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> $html 281 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
282 echo "</div>" >> $html 282 echo "</div>" >> "$html"
283 echo "</div>" >> $html 283 echo "</div>" >> "$html"
284 echo "</html>" >> $html 284 echo "</html>" >> "$html"
285 done < triplets.txt 285 done < triplets.txt
286 rm tmp.txt 286 rm tmp.txt
287 287
288 288
289 html="index.html" 289 html="index.html"
290 290
291 echo "</table>" >> $html 291 echo "</table>" >> "$html"
292 echo "</html>" >> $html 292 echo "</html>" >> "$html"
293 293