|
0
|
1 <!DOCTYPE html>
|
|
|
2 <html lang="en">
|
|
|
3 <head>
|
|
|
4 <meta charset="utf-8">
|
|
|
5 <meta http-equiv="X-UA-Compatible" content="IE=edge">
|
|
|
6 <meta name="viewport" content="width=device-width, initial-scale=1">
|
|
|
7 <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
|
|
|
8 <meta name="description" content="">
|
|
|
9 <meta name="author" content="">
|
|
|
10 <title>[BICH464] Phage QC on {{record_name}} - {{score}}</title>
|
|
|
11 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css">
|
|
|
12 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap-theme.min.css">
|
|
|
13
|
|
|
14 <style type="text/css">
|
|
|
15 /*
|
|
|
16 * Base structure
|
|
|
17 */
|
|
|
18
|
|
|
19 /* Move down content because we have a fixed navbar that is 50px tall */
|
|
|
20 body {
|
|
|
21 padding-top: 50px;
|
|
|
22 }
|
|
|
23
|
|
|
24 h3:before {
|
|
|
25 display: block;
|
|
|
26 content: " ";
|
|
|
27 margin-top: -50px;
|
|
|
28 height: 50px;
|
|
|
29 visibility: hidden;
|
|
|
30 }
|
|
|
31
|
|
|
32 /*
|
|
|
33 * Global add-ons
|
|
|
34 */
|
|
|
35
|
|
|
36 .sub-header {
|
|
|
37 padding-bottom: 10px;
|
|
|
38 border-bottom: 1px solid #eee;
|
|
|
39 }
|
|
|
40
|
|
|
41 /*
|
|
|
42 * Top navigation
|
|
|
43 * Hide default border to remove 1px line.
|
|
|
44 */
|
|
|
45 .navbar-fixed-top {
|
|
|
46 border: 0;
|
|
|
47 }
|
|
|
48
|
|
|
49 /*
|
|
|
50 * Sidebar
|
|
|
51 */
|
|
|
52
|
|
|
53 /* Hide for mobile, show later */
|
|
|
54 .sidebar {
|
|
|
55 display: none;
|
|
|
56 }
|
|
|
57 @media (min-width: 768px) {
|
|
|
58 .sidebar {
|
|
|
59 position: fixed;
|
|
|
60 top: 51px;
|
|
|
61 bottom: 0;
|
|
|
62 left: 0;
|
|
|
63 z-index: 1000;
|
|
|
64 display: block;
|
|
|
65 padding: 20px;
|
|
|
66 overflow-x: hidden;
|
|
|
67 overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
|
|
|
68 background-color: #f5f5f5;
|
|
|
69 border-right: 1px solid #eee;
|
|
|
70 }
|
|
|
71 }
|
|
|
72
|
|
|
73 /* Sidebar navigation */
|
|
|
74 .nav-sidebar {
|
|
|
75 margin-right: -21px; /* 20px padding + 1px border */
|
|
|
76 margin-bottom: 20px;
|
|
|
77 margin-left: -20px;
|
|
|
78 }
|
|
|
79 .nav-sidebar > li > a {
|
|
|
80 padding-right: 20px;
|
|
|
81 padding-left: 20px;
|
|
|
82 }
|
|
|
83 .nav-sidebar > .active > a,
|
|
|
84 .nav-sidebar > .active > a:hover,
|
|
|
85 .nav-sidebar > .active > a:focus {
|
|
|
86 color: #fff;
|
|
|
87 background-color: #428bca;
|
|
|
88 }
|
|
|
89
|
|
|
90
|
|
|
91 /*
|
|
|
92 * Main content
|
|
|
93 */
|
|
|
94
|
|
|
95 .main {
|
|
|
96 padding: 20px;
|
|
|
97 }
|
|
|
98 @media (min-width: 768px) {
|
|
|
99 .main {
|
|
|
100 padding-right: 40px;
|
|
|
101 padding-left: 40px;
|
|
|
102 }
|
|
|
103 }
|
|
|
104 .main .page-header {
|
|
|
105 margin-top: 0;
|
|
|
106 }
|
|
|
107
|
|
|
108
|
|
|
109 /*
|
|
|
110 * Placeholder dashboard ideas
|
|
|
111 */
|
|
|
112
|
|
|
113 .placeholders {
|
|
|
114 margin-bottom: 30px;
|
|
|
115 text-align: center;
|
|
|
116 }
|
|
|
117 .placeholders h4 {
|
|
|
118 margin-bottom: 0;
|
|
|
119 }
|
|
|
120 .placeholder {
|
|
|
121 margin-bottom: 20px;
|
|
|
122 }
|
|
|
123 .placeholder img {
|
|
|
124 display: inline-block;
|
|
|
125 border-radius: 50%;
|
|
|
126 }
|
|
|
127
|
|
|
128
|
|
|
129
|
|
|
130
|
|
|
131
|
|
|
132
|
|
|
133
|
|
|
134 /* CUSTOM CSS */
|
|
|
135 .spark {
|
|
|
136 position: relative;
|
|
|
137 margin:5px;
|
|
|
138 }
|
|
|
139 .spark span {
|
|
|
140 padding: 0px;
|
|
|
141 padding-left: 20px;
|
|
|
142 padding-right: 20px;
|
|
|
143 margin: 5px;
|
|
|
144 position: relative;
|
|
|
145 }
|
|
|
146 .spark .plus {
|
|
|
147 top: -10px;
|
|
|
148 background: #aaaaff;
|
|
|
149 }
|
|
|
150 .spark .minus {
|
|
|
151 top: 10px;
|
|
|
152 background: #ffaaaa;
|
|
|
153 }
|
|
|
154 .plus-focus {
|
|
|
155 top: -10px;
|
|
|
156 background: blue;
|
|
|
157 }
|
|
|
158 .minus-focus {
|
|
|
159 top: 10px;
|
|
|
160 background: red;
|
|
|
161 }
|
|
|
162 </style>
|
|
|
163 <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
|
|
|
164 <!--[if lt IE 9]>
|
|
|
165 <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
|
|
|
166 <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
|
|
167 <![endif]-->
|
|
|
168 </head>
|
|
|
169 <body>
|
|
|
170
|
|
|
171 <nav class="navbar navbar-inverse navbar-fixed-top">
|
|
|
172 <div class="container-fluid">
|
|
|
173 <div class="navbar-header">
|
|
|
174 <a class="navbar-brand" href="#">[BICH464] Phage QC on {{record_name}}</a>
|
|
|
175 </div>
|
|
|
176 </div>
|
|
|
177 </nav>
|
|
|
178
|
|
|
179 <div class="container-fluid">
|
|
|
180 <div class="row">
|
|
|
181 <div class="col-sm-3 col-md-2 sidebar">
|
|
|
182 <ul class="nav nav-sidebar">
|
|
|
183 <li><a href="#main"><b>Overview</b></a></li>
|
|
|
184 <li><a href="#bad_gene_starts"><b>Bad Gene Starts</b></a></li>
|
|
|
185 <li><a href="#missing_rbs"><small>Missing RBS</small></a></li>
|
|
|
186 <li><a href="#weird_starts"><small>Unusual Start Codons</small></a></li>
|
|
|
187 <li><a href="#excessive_gaps"><small>Excessive Gaps</small></a></li>
|
|
|
188 <li><a href="#excessive_overlap"><small>Excessive Overlaps</small></a></li>
|
|
|
189 <!--<li><a href="#coding_density"><small>Coding Density</small></a></li>-->
|
|
|
190 <li><a href="#gene_model"><b>Gene Model Issues</b></a></li>
|
|
|
191 </ul>
|
|
|
192 </div>
|
|
|
193 <div class="col-sm-9 col-sm-offset-3 col-md-10 col-md-offset-2 main" id="main">
|
|
|
194 <div class="jumbotron">
|
|
|
195 <div class="row">
|
|
|
196 <div class="col-sm-7">
|
|
|
197 <h1>Phage {{record_name}}</h1>
|
|
|
198 <!--<h2>Score: {{ '%d' % ((gene_model_score + coding_density + excessive_overlap_score + excessive_overlap_score + missing_rbs_score) / 5)}}</h2>-->
|
|
|
199 </div>
|
|
|
200 <!--<div class="col-sm-5">
|
|
|
201 <table class="table table-striped">
|
|
|
202 <thead>
|
|
|
203 <tr>
|
|
|
204 <th>Section</th>
|
|
|
205 <th>Score</th>
|
|
|
206 </tr>
|
|
|
207 </thead>
|
|
|
208 <tbody>
|
|
|
209 <tr><td>Missing RBS</td><td>{{ '%d' % missing_rbs_score }}%</td></tr>
|
|
|
210 <tr><td>Excessive Gaps</td><td>{{ '%d' % excessive_gap_score }}%</td></tr>
|
|
|
211 <tr><td>Excessive Overlap</td><td>{{ '%d' % excessive_overlap_score }}%</td></tr>
|
|
|
212 <tr><td>Coding Density Score</td><td>{{ '%d' % coding_density }}%</td></tr>
|
|
|
213 <tr><td>Coding Density Real</td><td>{{ '%0.2f' % (100 * coding_density_exact) }}%</td></tr>
|
|
|
214 <tr><td>Gene Model Issues</td><td>{{ '%d' % gene_model_score }}%</td></tr>
|
|
|
215 </tbody>
|
|
|
216 </table>
|
|
|
217 </div>-->
|
|
|
218 </div>
|
|
|
219 <div class="row">
|
|
|
220 <h3>Genome Overview</h3>
|
|
|
221 <h4>Genes</h4>
|
|
|
222 <ul>
|
|
|
223 <li>Count: {{ genome_overview.genes.count }}</li>
|
|
|
224 <li>Bases: {{ genome_overview.genes.bases }}</li>
|
|
|
225 <li>Average Length: {{ genome_overview.genes.avg_len | round | int}}</li>
|
|
|
226 <li>Coding Density: {{ '%0.2f' % (100 * coding_density_exact) }}%</li>
|
|
|
227 <li>Composition
|
|
|
228 <ul>
|
|
|
229 <li>A {{ genome_overview.genes.comp.A }}</li>
|
|
|
230 <li>C {{ genome_overview.genes.comp.C }}</li>
|
|
|
231 <li>T {{ genome_overview.genes.comp.T }}</li>
|
|
|
232 <li>G {{ genome_overview.genes.comp.G }}</li>
|
|
|
233 </ul>
|
|
|
234 </li>
|
|
|
235 </ul>
|
|
|
236 <h4>Overall</h4>
|
|
|
237 <ul>
|
|
|
238 <li>%GC: {{ '%0.2f' % (100 * genome_overview.overall.gc) }}%</li>
|
|
|
239 <li>Composition
|
|
|
240 <ul>
|
|
|
241 <li>A {{ genome_overview.overall.comp.A }}</li>
|
|
|
242 <li>C {{ genome_overview.overall.comp.C }}</li>
|
|
|
243 <li>T {{ genome_overview.overall.comp.T }}</li>
|
|
|
244 <li>G {{ genome_overview.overall.comp.G }}</li>
|
|
|
245 </ul>
|
|
|
246 </li>
|
|
|
247 </ul>
|
|
|
248 </div>
|
|
|
249 </div>
|
|
|
250
|
|
|
251 <h2 class="sub-header" id="bad_gene_starts">Gene Starts</h2>
|
|
|
252 <h3 id="missing_rbs">Genes Missing RBS <small>{{missing_rbs_good}} / {{missing_rbs_good + missing_rbs_bad}}</small></h3>
|
|
|
253 <p>The following genes have issues with their RBS.</p>
|
|
|
254 {% if not rbss_annotated %}
|
|
|
255 <p>
|
|
|
256 Since you have not annotated any possible RBSs, this does not count off from your overall score.
|
|
|
257 </p>
|
|
|
258 {% endif %}
|
|
|
259 <div class="table-responsive">
|
|
|
260 <table class="table table-striped">
|
|
|
261 <thead>
|
|
|
262 <tr>
|
|
|
263 <th>ID</th>
|
|
|
264 <th>Location</th>
|
|
|
265 <th>Error</th>
|
|
|
266 <th>Upstream (-{{upstream_max}} .. -{{upstream_min}})</th>
|
|
|
267 </tr>
|
|
|
268 </thead>
|
|
|
269 <tbody>
|
|
|
270 {% for row in missing_rbs %}
|
|
|
271 {% if "None found" in row.__message %}
|
|
|
272 <tr>
|
|
|
273 <td>{{row | nice_id | decode}}</td>
|
|
|
274 <td>{{row.location.start}}..{{row.location.end}} [{{row.strand}}]</td>
|
|
|
275 <td>None found</td>
|
|
|
276 <td><span style="font-family:monospace">{{row.__upstream }}</span></td>
|
|
|
277 </tr>
|
|
|
278 {% endif %}
|
|
|
279 {% endfor %}
|
|
|
280 </tbody>
|
|
|
281 </table>
|
|
|
282 </div>
|
|
|
283
|
|
|
284 <h3 id="weird_starts">Start Codon Usage</h3>
|
|
|
285 <p>This section covers genes with unusual start codons</p>
|
|
|
286 <div class="table-responsive">
|
|
|
287 <table class="table table-striped">
|
|
|
288 <thead>
|
|
|
289 <tr>
|
|
|
290 <th>Start Codon</th>
|
|
|
291 <th>Count</th>
|
|
|
292 </tr>
|
|
|
293 </thead>
|
|
|
294 <tbody>
|
|
|
295 {% for codon_key in weird_starts_overall_sorted_keys %}
|
|
|
296 <tr><td>{{ codon_key }}</td><td>{{ weird_starts_overall[codon_key] }}</td></tr>
|
|
|
297 {% endfor %}
|
|
|
298 </tbody>
|
|
|
299 </table>
|
|
|
300 </div>
|
|
|
301
|
|
|
302 <div class="table-responsive">
|
|
|
303 <table class="table table-striped">
|
|
|
304 <thead>
|
|
|
305 <tr>
|
|
|
306 <th>ID</th>
|
|
|
307 <th>Location</th>
|
|
|
308 <th>Error</th>
|
|
|
309 </tr>
|
|
|
310 </thead>
|
|
|
311 <tbody>
|
|
|
312 {% for row in weird_starts %}
|
|
|
313 <tr>
|
|
|
314 <td>{{row | nice_id| decode}}</td>
|
|
|
315 <td>{{row.location.start}}..{{row.location.end}} [{{row.strand}}]</td>
|
|
|
316 <td>{{row.qualifiers.get('note', [])}}</td>
|
|
|
317 </tr>
|
|
|
318 {% endfor %}
|
|
|
319 </tbody>
|
|
|
320 </table>
|
|
|
321 </div>
|
|
|
322
|
|
|
323 <h3 id="excessive_gaps">Intergenic Gaps</h3>
|
|
|
324 <p>Phage genomes are under pressure to maintain high coding density. Large intergenic gaps may be a sign of incorrect gene starts or missing genes.</p>
|
|
|
325 <div class="table-responsive">
|
|
|
326 <table class="table table-striped">
|
|
|
327 <thead>
|
|
|
328 <tr>
|
|
|
329 <th>Region</th>
|
|
|
330 <th>Size</th>
|
|
|
331 <th>Bounding Gene Transcription Direction</th>
|
|
|
332 <th>Message</th>
|
|
|
333 </tr>
|
|
|
334 </thead>
|
|
|
335 <tbody>
|
|
|
336 {% for row in excessive_gap %}
|
|
|
337 <tr>
|
|
|
338 <td>{{row[0]}} .. {{row[1]}}</td>
|
|
|
339 <td>{{row[1] - row[0]}}</td>
|
|
|
340 <td>{{row[2] | nice_strand}} {{row[3] | nice_strand}}</td>
|
|
|
341 <td>
|
|
|
342 {% if row[4] == 0 %}
|
|
|
343 {% else %}
|
|
|
344 {{row[4]}} possible genes found in this region
|
|
|
345 {% endif %}
|
|
|
346 </td>
|
|
|
347 </tr>
|
|
|
348 {% endfor %}
|
|
|
349 </tbody>
|
|
|
350 </table>
|
|
|
351 </div>
|
|
|
352
|
|
|
353 <h3 id="excessive_overlap">Overlapping Genes</h3>
|
|
|
354 <p>Large gene overlaps may indicate an incorrect gene start or miscalled gene.</p>
|
|
|
355 <div class="table-responsive">
|
|
|
356 <table class="table table-striped">
|
|
|
357 <thead>
|
|
|
358 <tr>
|
|
|
359 <th>Feature A</th>
|
|
|
360 <th>Feature B</th>
|
|
|
361 <th>Shared Region</th>
|
|
|
362 <th>Overlap Length</th>
|
|
|
363 </tr>
|
|
|
364 </thead>
|
|
|
365 <tbody>
|
|
|
366 {% for row in excessive_overlap %}
|
|
|
367 <tr>
|
|
|
368 <td>{{row[0] | nice_id | decode}} ({{row[0].location}})</td>
|
|
|
369 <td>{{row[1] | nice_id | decode}} ({{row[1].location}})</td>
|
|
|
370 <td>{{row[2]}}..{{row[3]}}</td>
|
|
|
371 <td>{{row[3] - row[2]}}bp</td>
|
|
|
372 </tr>
|
|
|
373 {% endfor %}
|
|
|
374 </tbody>
|
|
|
375 </table>
|
|
|
376 </div>
|
|
|
377 <!--<h3 id="coding_density">Coding Density Issues <small>{{ coding_density }} / 100</small></h3>
|
|
|
378 <div class="table-responsive">
|
|
|
379 <p>
|
|
|
380 You have a coding density score of {{ coding_density_real }} which scores
|
|
|
381 {{ coding_density }} / 100. Most genomes should be in the 90% to
|
|
|
382 100% coding density range. Your exact coding density is {{ coding_density_exact }}.
|
|
|
383 </p>
|
|
|
384 </div>-->
|
|
|
385
|
|
|
386 <h2 class="sub-header" id="gene_model">Gene Model Issues</h2>
|
|
|
387 <p>These issues are mostly derived from how Apollo handles the gene model. <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAMsAAAAUCAYAAAAjk8nJAAAABmJLR0QA/wD/AP+gvaeTAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH4AIRECEhlCV0dQAAAPBJREFUaN7t20EKgkAUxvFnlBASiBewNm7HldA+ukQH6AhtukBH6ABdIqJtIIS6dVNdoCtMm8CN1gtb6f+3GmQ28/DjzeDoWGutAPhqQAkAnSElQB0n6M9a7ZOwoKV43/015uuWnWW2q8a3Tf1zgDML0DNpepSyvLTfhh1OFBMd34rldzEmlCw7i+eNJYrmnFmAJkXxEBH5GBrCAihDQ1gAZWg44ANKdBaghjGhuO6IbRjwS0joLIAyJOqwrBbVeHulqOieOJ6K708aQ0JnAd6SZKma5/A/C2pfjKA/Fym1t44JCxrD0heEBfgzPkoCSi/B1kHb2fpwrwAAAABJRU5ErkJggg=="></p>
|
|
|
388 <div class="table-responsive">
|
|
|
389 <table class="table table-striped">
|
|
|
390 <thead>
|
|
|
391 <tr>
|
|
|
392 <th>ID</th>
|
|
|
393 <th>Exon</th>
|
|
|
394 <th>CDS</th>
|
|
|
395 <th>Message</th>
|
|
|
396 </tr>
|
|
|
397 </thead>
|
|
|
398 <tbody>
|
|
|
399 {% for row in gene_model %}
|
|
|
400 <tr>
|
|
|
401 <td>{{row[0]}}</td>
|
|
|
402 <td>{{row[1].location}}</td>
|
|
|
403 <td>{{row[2].location}}</td>
|
|
|
404 <td>{{row[3]}}</td>
|
|
|
405 </tr>
|
|
|
406 {% endfor %}
|
|
|
407 </tbody>
|
|
|
408 </table>
|
|
|
409 </div>
|
|
|
410
|
|
|
411 </div>
|
|
|
412 </div>
|
|
|
413 </div>
|
|
|
414
|
|
|
415
|
|
|
416 <script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
|
|
|
417 </body>
|
|
|
418 </html>
|
|
|
419
|
