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author davidmurphy
date Fri, 13 Jan 2012 07:18:19 -0500
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3:09d2dac9ef73 4:4d47ab2b7bcc
1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
2 "http://www.w3.org/TR/html4/transitional.dtd">
3 <html>
4 <head>
5 <link rel="stylesheet" type="text/css" href="logo.css" >
6
7 <title>CodonLogo - Tests </title>
8 <meta name="author" content="Gavin E. Crooks" >
9 <meta name="ID" content="$ID:" >
10
11 <style type="text/css">
12 td {
13 border-left : white solid 4pt
14 }
15 .error {
16 color: #900;
17 border-left: red solid +4pt;
18 }
19
20 .err_msg {
21 color: #900;
22 }
23
24 </style>
25 </head>
26
27 <body style="align:center">
28
29
30 <table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
31 <tr><td >
32 <h1> CodonLogo: Tests</h1>
33
34 </td><td align = "right">
35 &middot;
36 <a href="./">about</a>&nbsp;&middot;
37 <a href="create.cgi">create</a>&nbsp;&middot;
38 <a href="examples.html">examples</a>&nbsp;&middot;
39 <a href="manual.html">manual</a>&nbsp;&middot;
40 <br>
41 &nbsp;
42 </td></tr>
43
44 <tr><td colspan='2'>
45
46 Various tests of the CodonLogo webapp. <br >
47
48 <hr >
49
50 <dl>
51 <dt>Relative Entropy Test</dt>
52 <dd>
53 The entropy should be 2 bits, 1 bit, 0 bits
54 (The small sample correction should be turned off.)
55 <br >
56 <form method="post" action="create.cgi">
57 <input type="submit" name="cmd_edit" value="Edit" >
58 <input type="submit" name="cmd_create" value="Create" >
59 <input type="hidden" name="show_yaxis" value="true" >
60 <input type="hidden" name="show_xaxis" value="true" >
61 <input type="hidden" name="show_fineprint" value="true" >
62 <input type="hidden" name="show_errorbars" value="true" >
63 <input type="hidden" name="download" value="true" >
64 <input type="hidden" name="composition" value="comp_none" >
65
66 <input type="hidden" name="sequences" value=
67 ">
68 GTTGTTGTTGTT
69 >
70 GTCGTCGTCGTC
71 >
72 GGGGGGGGGGGG
73 >
74 GGAGGAGGAGGA
75 " >
76 </form>
77 </dd>
78
79
80 <dt>Title And Labels Test</dt>
81 <dd>
82 Replace and display x-label, y-label and title.
83 <form method="post" action="create.cgi">
84 <input type="submit" name="cmd_edit" value="Edit" >
85 <input type="submit" name="cmd_create" value="Create" >
86 <input type="hidden" name="show_yaxis" value="true" >
87 <input type="hidden" name="show_xaxis" value="true" >
88 <input type="hidden" name="show_fineprint" value="true" >
89 <input type="hidden" name="show_errorbars" value="true" >
90 <input type="hidden" name="download" value="true" >
91
92 <input type="hidden" name="yaxis_label" value="The Y-axis" >
93 <input type="hidden" name="xaxis_label" value="The X-axis" >
94 <input type="hidden" name="logo_title" value="This is the TITLE" >
95 <input type="hidden" name="sequences" value=
96 ">
97 AAAGTGAAAGTGAAAGTGAAAGTG
98 >
99 AAAGCGAAAGCGAAAGCGAAAGCG
100 >
101 TGCCCTTGCCCTTGCCCTTGCCCT
102 >
103 TGCCTTTGCCTTTGCCTTTGCCTT
104 " >
105 </form>
106
107 Same, but do not show axes
108 <form method="post" action="create.cgi">
109 <input type="submit" name="cmd_edit" value="Edit" >
110 <input type="submit" name="cmd_create" value="Create" >
111 <input type="hidden" name="show_fineprint" value="true" >
112 <input type="hidden" name="show_errorbars" value="true" >
113 <input type="hidden" name="download" value="true" >
114
115 <input type="hidden" name="yaxis_label" value="This is the Y-axis" >
116 <input type="hidden" name="xaxis_label" value="This is the X-axis" >
117 <input type="hidden" name="logo_title" value="This is the TITLE" >
118 <input type="hidden" name="sequences" value=
119 ">
120 AAAGTGAAAGTGAAAGTGAAAGTG
121 >
122 AAAGCGAAAGCGAAAGCGAAAGCG
123 >
124 TGCCCTTGCCCTTGCCCTTGCCCT
125 >
126 TGCCTTTGCCTTTGCCTTTGCCTT
127 " >
128 </form>
129 </dd>
130
131
132
133 <dt>Format Test</dt>
134 <dd>
135 Ensure that this logo can be created in each of the available formats
136 <form method="post" action="create.cgi">
137 <input type="submit" name="cmd_edit" value="Edit" >
138 <input type="submit" name="cmd_create" value="Create" >
139 <input type="hidden" name="show_yaxis" value="true" >
140 <input type="hidden" name="show_xaxis" value="true" >
141 <input type="hidden" name="show_fineprint" value="true" >
142 <input type="hidden" name="show_errorbars" value="true" >
143 <input type="hidden" name="download" value="true" >
144
145 Format: <select name="format">
146 <option value="png_print">PNG</option>
147 <option value="png">PNG (low res.)</option>
148 <option value="jpeg">JPEG (low res.)</option>
149 <option value="eps">EPS (vector)</option>
150 <option value="pdf">PDF (vector)</option>
151 <option value="txt">data</option>
152 </select>
153
154 <input type="hidden" name="sequences" value=
155 ">
156 AAAGTGAAAGTGAAAGTGAAAGTG
157 >
158 AAAGCGAAAGCGAAAGCGAAAGCG
159 >
160 TGCCCTTGCCCTTGCCCTTGCCCT
161 >
162 TGCCTTTGCCTTTGCCTTTGCCTT
163 " >
164 </form>
165 </dd>
166
167
168
169
170 <dt>Test Alphabetic Order</dt>
171 <dd>
172 Each character in each stack has the same entropy. The letters
173 should be alphabetized, top down.
174 <form method="post" action="create.cgi">
175 <input type="submit" name="cmd_edit" value="Edit" >
176 <input type="submit" name="cmd_create" value="Create" >
177 <input type="hidden" name="show_yaxis" value="true" >
178 <input type="hidden" name="show_xaxis" value="true" >
179 <input type="hidden" name="show_fineprint" value="true" >
180 <input type="hidden" name="show_errorbars" value="true" >
181 <input type="hidden" name="download" value="true" >
182 <input type="hidden" name="composition" value="comp_none" >
183 (NA)
184 <input type="hidden" name="sequences" value=
185 ">
186 AAAGTG
187 >
188 AAAGCG
189 >
190 TGCCCT
191 >
192 TGCCTT
193 " >
194 </form>
195
196 <form method="post" action="create.cgi">
197 <input type="submit" name="cmd_edit" value="Edit" >
198 <input type="submit" name="cmd_create" value="Create" >
199 <input type="hidden" name="show_yaxis" value="true" >
200 <input type="hidden" name="show_xaxis" value="true" >
201 <input type="hidden" name="show_fineprint" value="true" >
202 <input type="hidden" name="show_errorbars" value="true" > (AA)
203 <input type="hidden" name="download" value="true" >
204 <input type="hidden" name="sequences" value=
205 ">
206 CA
207 >
208 CA
209 >
210 VA
211 >
212 VG
213 >
214 KG
215 >
216 KG
217 " >
218 </form>
219 </dd>
220
221
222
223 <dt>One Single Column</dt>
224 <dd>
225 Should not die just because there is only 1 stack.
226 <form method="post" action="create.cgi">
227 <input type="submit" name="cmd_edit" value="Edit" >
228 <input type="submit" name="cmd_create" value="Create" >
229 <input type="hidden" name="download" value="true" >
230 <input type="hidden" name="sequences" value=
231 ">
232 A
233 >
234 A
235 >
236 G
237 >
238 G
239 >
240 G
241 >
242 G
243 " >
244 </form>
245 </dd>
246
247
248 <dt> Small Sample Correction Test</dt>
249 <dd>
250 The samples per column decrease from 32 (left) to 1 (right).
251 Before the small sample correction the relative entropy of each stack
252 is 2 bits.
253 <form method="post" action="create.cgi">
254 <input type="submit" name="cmd_edit" value="Edit" >
255 <input type="submit" name="cmd_create" value="Create" >
256 <input type="hidden" name="show_yaxis" value="true" >
257 <input type="hidden" name="show_xaxis" value="true" >
258 <input type="hidden" name="download" value="true" >
259 <input type="hidden" name="show_fineprint" value="true" >
260 <select name="composition" >
261 <option value = "comp_none" >No adjustment for composition</option>
262 <option value = "comp_auto" >auto</option>
263 </select>
264
265 <input type="hidden" name="sequences" value=
266 ">
267 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
268 >
269 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-
270 >
271 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--
272 >
273 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG---
274 >
275 GGGGGGGGGGGGGGGGGGGGGGGGGGGG----
276 >
277 GGGGGGGGGGGGGGGGGGGGGGGGGGG-----
278 >
279 GGGGGGGGGGGGGGGGGGGGGGGGGG------
280 >
281 GGGGGGGGGGGGGGGGGGGGGGGGG-------
282 >
283 GGGGGGGGGGGGGGGGGGGGGGGG--------
284 >
285 GGGGGGGGGGGGGGGGGGGGGGG---------
286 >
287 GGGGGGGGGGGGGGGGGGGGGG----------
288 >
289 GGGGGGGGGGGGGGGGGGGGG-----------
290 >
291 GGGGGGGGGGGGGGGGGGGG------------
292 >
293 GGGGGGGGGGGGGGGGGGG-------------
294 >
295 GGGGGGGGGGGGGGGGGG--------------
296 >
297 GGGGGGGGGGGGGGGG----------------
298 >
299 GGGGGGGGGGGGGGG-----------------
300 >
301 GGGGGGGGGGGGGG------------------
302 >
303 GGGGGGGGGGGGG-------------------
304 >
305 GGGGGGGGGGGG--------------------
306 >
307 GGGGGGGGGGG---------------------
308 >
309 GGGGGGGGGG----------------------
310 >
311 GGGGGGGGG-----------------------
312 >
313 GGGGGGGG------------------------
314 >
315 GGGGGGG-------------------------
316 >
317 GGGGGG--------------------------
318 >
319 GGGGG---------------------------
320 >
321 GGGG----------------------------
322 >
323 GGG-----------------------------
324 >
325 GG------------------------------
326 >
327 G-------------------------------
328 " >
329 </form>
330 </dd>
331
332
333
334 <dt> Test Graceful Failure</dt>
335 <dd>
336 Each of these tests should result in a polite and informative error message.
337 <form method="post" action="create.cgi">
338 <input type="submit" name="cmd_create" value="Fail: No sequence data" >
339 <input type="hidden" name="show_yaxis" value="true" >
340 <input type="hidden" name="show_xaxis" value="true" >
341 <input type="hidden" name="show_fineprint" value="true" >
342 <input type="hidden" name="download" value="true" >
343 <input type="hidden" name="show_errorbars" checked="checked" >
344 <input type="hidden" name="sequences" value="" >
345 </form>
346
347 <form method="post" action="create.cgi">
348 <input type="submit" name="cmd_create" value="Fail: Malformed sequences" >
349 <input type="hidden" name="show_yaxis" value="true" >
350 <input type="hidden" name="download" value="true" >
351 <input type="hidden" name="show_xaxis" value="true" >
352 <input type="hidden" name="show_fineprint" value="true" >
353 <input type="hidden" name="show_errorbars" checked="checked" >
354 <input type="hidden" name="sequences" value="
355 asdajksgh
356 >
357 GGGGGGGGGGGGGG------------------
358 >
359 GGGGGGGGGGGGG-------------------
360 >
361 " >
362 </form>
363
364 <form method="post" action="create.cgi">
365 <input type="submit" name="cmd_create" value="Fail: Unknown format" >
366 <input type="hidden" name="format" value="NO_SUCH_FORMAT" >
367 <input type="hidden" name="show_yaxis" value="true" >
368 <input type="hidden" name="show_xaxis" value="true" >
369 <input type="hidden" name="show_fineprint" value="true" >
370 <input type="hidden" name="show_errorbars" checked="checked" >
371 <input type="hidden" name="download" value="true" >
372 <input type="hidden" name="sequences" value=">
373 GGGGGGGGGGGGGG------------------
374 >
375 GGGGGGGGGGGGG-------------------
376 >
377 " >
378 </form>
379
380 <form method="post" action="create.cgi">
381 <input type="submit" name="cmd_create" value="Fail: Malformed data" >
382 <input type="hidden" name="show_yaxis" value="true" >
383 <input type="hidden" name="show_xaxis" value="true" >
384 <input type="hidden" name="download" value="true" >
385 <input type="hidden" name="show_fineprint" value="true" >
386 <input type="hidden" name="show_errorbars" checked="checked" >
387 <input type="hidden" name="sequences" value=">
388 GGGGGGGGGGGGGG------------------
389 >
390 GGGGGGGGGGGGG------------------
391 >
392 " >
393 </form>
394
395
396 </dd>
397
398
399
400 <dt> Logos Sizes</dt>
401 <dd>
402 Same sequences, three different sizes.
403 <form method="post" action="create.cgi">
404 <input type="submit" name="cmd_edit" value="Edit" >
405 <input type="hidden" name="download" value="true" >
406 <input type="submit" name="cmd_create" value="Create" >
407 <input type="hidden" name="show_yaxis" value="true" >
408 <input type="hidden" name="show_xaxis" value="true" >
409 <input type="hidden" name="show_fineprint" value="true" >
410 Size:
411 <select name="size" >
412 <option selected="selected" >small</option>
413 <option >medium</option>
414 <option >large</option>
415 </select>
416
417
418 <input type="hidden" name="sequences" value=
419 ">aldB -18->4
420 attcgtgatagctgtcgtaaag
421 >ansB 103->125
422 ttttgttacctgcctctaactt
423 >araB1 109->131
424 aagtgtgacgccgtgcaaataa
425 >araB2 147->169
426 tgccgtgattatagacactttt
427 >cdd 1 107->129
428 atttgcgatgcgtcgcgcattt
429 >cdd 2 57->79
430 taatgagattcagatcacatat
431 >crp 1 115->137
432 taatgtgacgtcctttgcatac
433 >crp 2
434 gaaggcgacctgggtcatgctg
435 >cya 151->173
436 aggtgttaaattgatcacgttt
437 >cytR 1 125->147
438 cgatgcgaggcggatcgaaaaa
439 >cytR 2 106->128
440 aaattcaatattcatcacactt
441 >dadAX 1 95->117
442 agatgtgagccagctcaccata
443 >dadAX 2 32->54
444 agatgtgattagattattattc
445 >deoP2 1 75->97
446 aattgtgatgtgtatcgaagtg
447 >deoP2 2 128->150
448 ttatttgaaccagatcgcatta
449 >fur 136->158
450 aaatgtaagctgtgccacgttt
451 >gal 56->78
452 aagtgtgacatggaataaatta
453 >glpACB (glpTQ) 1 54->76
454 ttgtttgatttcgcgcatattc
455 >glpACB (glpTQ) 2 94->116
456 aaacgtgatttcatgcgtcatt
457 >glpACB (glpTQ) 144->166
458 atgtgtgcggcaattcacattt
459 >glpD (glpE) 95->117
460 taatgttatacatatcactcta
461 >glpFK 1 120->142
462 ttttatgacgaggcacacacat
463 >glpFK 2 95->117
464 aagttcgatatttctcgttttt
465 >gut (srlA) 72->94
466 ttttgcgatcaaaataacactt
467 >ilvB 87->109
468 aaacgtgatcaacccctcaatt
469 >lac 1 (lacZ) 88->110
470 taatgtgagttagctcactcat
471 >lac 2 (lacZ) 16->38
472 aattgtgagcggataacaattt
473 >malEpKp1 110->132
474 ttgtgtgatctctgttacagaa
475 >malEpKp2 139->161
476 TAAtgtggagatgcgcacaTAA
477 >malEpKp3 173->195
478 TTTtgcaagcaacatcacgAAA
479 >malEpKp4 205->227
480 GACctcggtttagttcacaGAA
481 >malT 121->143
482 aattgtgacacagtgcaaattc
483 >melR 52->74
484 aaccgtgctcccactcgcagtc
485 >mtl 302->324
486 TCTTGTGATTCAGATCACAAAG
487 >nag 156->178
488 ttttgtgagttttgtcaccaaa
489 >nupG2 97->119
490 aaatgttatccacatcacaatt
491 >nupG1 47->69
492 ttatttgccacaggtaacaaaa
493 >ompA 166->188
494 atgcctgacggagttcacactt
495 >ompR 161->183
496 taacgtgatcatatcaacagaa
497 >ptsH A 316->338
498 Ttttgtggcctgcttcaaactt
499 >ptsH B 188->210
500 ttttatgatttggttcaattct
501 >rhaS (rhaB) 161->183
502 aattgtgaacatcatcacgttc
503 >rot 1 (ppiA) 182->204
504 ttttgtgatctgtttaaatgtt
505 >rot 2 (ppiA) 129->151
506 agaggtgattttgatcacggaa
507 >tdcA 60->82
508 atttgtgagtggtcgcacatat
509 >tnaL 73->95
510 gattgtgattcgattcacattt
511 >tsx 2 146->168
512 gtgtgtaaacgtgaacgcaatc
513 >tsx 1 107->129
514 aactgtgaaacgaaacatattt
515 >uxuAB 165->187
516 TCTTGTGATGTGGTTAACCAAT
517 " >
518 </form>
519 </dd>
520
521
522
523
524 </dl>
525
526
527
528 </td></tr>
529
530
531
532
533 </table>
534
535 <script type="text/javascript">
536 var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
537 document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
538 </script>
539 <script type="text/javascript">
540 var pageTracker = _gat._getTracker("UA-5951066-1");
541 pageTracker._trackPageview();
542 </script>
543 </body></html>