Mercurial > repos > jankanis > blast2html
comparison blast2html.html.jinja @ 22:efce16c98650
rename blast2html
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Thu, 15 May 2014 10:48:09 +0200 |
| parents | blast_html.html.jinja@9596fea636bb |
| children | 6995a6f34f3f |
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| 21:9596fea636bb | 22:efce16c98650 |
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| 1 <!DOCTYPE html> | |
| 2 <html> | |
| 3 <head> | |
| 4 <meta charset="UTF-8"> | |
| 5 <meta name=generator content="blast2html; see ..."> | |
| 6 | |
| 7 <title>Blast output</title> | |
| 8 | |
| 9 <style> | |
| 10 body { | |
| 11 color: #333333; | |
| 12 font-family: Arial,Sans-Serif; | |
| 13 } | |
| 14 | |
| 15 :link { | |
| 16 color: #336699; | |
| 17 } | |
| 18 | |
| 19 .right { | |
| 20 float: right; | |
| 21 } | |
| 22 | |
| 23 #content { | |
| 24 margin: 0 2em; | |
| 25 padding: 0.5em; | |
| 26 border: 1px solid #888888; | |
| 27 background-color: #d3dff5; | |
| 28 } | |
| 29 | |
| 30 h1, h2, h3, h4, h5, h6 { | |
| 31 color: #2A6979; | |
| 32 font-family: arial,verdana,sans-serif; | |
| 33 letter-spacing: -1px; | |
| 34 margin: 1.2em 0 0.3em; | |
| 35 } | |
| 36 | |
| 37 h1 { | |
| 38 border-bottom: 1px solid #CCCCCC; | |
| 39 font-size: 150%; | |
| 40 padding-bottom: 0.1em; | |
| 41 } | |
| 42 | |
| 43 h2 { | |
| 44 font-size: 120%; | |
| 45 font-weight: bold; | |
| 46 } | |
| 47 | |
| 48 h4.darkHeader { | |
| 49 color: #4D4D4D; | |
| 50 letter-spacing: 0; | |
| 51 font-weight: bold; | |
| 52 } | |
| 53 | |
| 54 #nodata { | |
| 55 font-weight: bold; | |
| 56 } | |
| 57 | |
| 58 .index { | |
| 59 margin-bottom: 3em; | |
| 60 } | |
| 61 .index div.indexentry { | |
| 62 margin: 1.2em 1.6em; | |
| 63 font-weight: bold; | |
| 64 font-size: 100%; | |
| 65 } | |
| 66 | |
| 67 .headerdata { | |
| 68 font-size: 90%; | |
| 69 } | |
| 70 .headerdata .param { | |
| 71 font-weight: bold; | |
| 72 text-align: right; | |
| 73 padding: 0 1em; | |
| 74 } | |
| 75 | |
| 76 .grey { | |
| 77 background-color: #eeeeee; | |
| 78 border: 1px solid #cccccc; | |
| 79 padding: 1em; | |
| 80 } | |
| 81 | |
| 82 .white { | |
| 83 background-color: white; | |
| 84 border: 1px solid #cccccc; | |
| 85 padding: 1.5em 2%; | |
| 86 } | |
| 87 | |
| 88 .graphicrow { | |
| 89 clear: left; | |
| 90 width: 100%; | |
| 91 } | |
| 92 | |
| 93 .graphicitem { | |
| 94 float: left; | |
| 95 } | |
| 96 | |
| 97 | |
| 98 | |
| 99 .graphics .grey { | |
| 100 text-align: center; | |
| 101 } | |
| 102 | |
| 103 .graphic { | |
| 104 background-color: white; | |
| 105 border: 2px solid black; | |
| 106 padding: 1.5em; | |
| 107 margin: auto; | |
| 108 } | |
| 109 | |
| 110 .centered, .defline, div.legend, div.tablewrapper { | |
| 111 margin-left: auto; | |
| 112 margin-right: auto; | |
| 113 } | |
| 114 | |
| 115 .defline { | |
| 116 background-color: white; | |
| 117 border: 1px solid black; | |
| 118 margin: .5em auto; | |
| 119 padding-left: .2em; | |
| 120 padding-right: .2em; | |
| 121 max-width: 50em; | |
| 122 text-align: left; | |
| 123 height: 2.8em; | |
| 124 overflow-y: hidden; | |
| 125 } | |
| 126 | |
| 127 div.legend { | |
| 128 max-width: 40em; | |
| 129 } | |
| 130 div.legend div { | |
| 131 width: 100%; | |
| 132 color: white; | |
| 133 font-weight: bold; | |
| 134 border-spacing: 0; | |
| 135 } | |
| 136 div.legend div .graphicitem { | |
| 137 width: 20%; | |
| 138 padding: 0; | |
| 139 margin: 0; | |
| 140 border: none; | |
| 141 } | |
| 142 | |
| 143 div.tablewrapper { | |
| 144 width: 50%; | |
| 145 min-width: 60em; | |
| 146 } | |
| 147 | |
| 148 /* For small widths we give the graphic 100% */ | |
| 149 @media (max-width: 72.5em) { | |
| 150 div.tablewrapper { | |
| 151 width: 100%; | |
| 152 min-width: 0px; | |
| 153 } | |
| 154 } | |
| 155 | |
| 156 .scale { | |
| 157 width: 100%; | |
| 158 margin: .5em 0; | |
| 159 font-weight: bold; | |
| 160 } | |
| 161 .scale div { | |
| 162 color: red; | |
| 163 text-align: left; | |
| 164 } | |
| 165 .scale .graphicrow { | |
| 166 margin: .5em 0 .5em 0; | |
| 167 color: white; | |
| 168 } | |
| 169 .scale .graphicitem { | |
| 170 position: relative; | |
| 171 } | |
| 172 .scale .graphicitem div { | |
| 173 margin: 0 1px; | |
| 174 padding: 0 2px; | |
| 175 text-align: right; | |
| 176 background-color: red; | |
| 177 color: white; | |
| 178 } | |
| 179 .scale .graphicitem:first-child div { | |
| 180 margin-left: 0px; | |
| 181 } | |
| 182 .scale .graphicitem:last-child div { | |
| 183 margin-right: 0px; | |
| 184 } | |
| 185 .scale .graphicitem .lastlabel { | |
| 186 position: absolute; | |
| 187 top: 0px; | |
| 188 left: 100%; | |
| 189 background-color: transparent; | |
| 190 color: red; | |
| 191 } | |
| 192 | |
| 193 a.matchresult { | |
| 194 display: block; | |
| 195 margin: 0; | |
| 196 padding: 0; | |
| 197 } | |
| 198 div.matchrow { | |
| 199 margin-top: 4px; | |
| 200 } | |
| 201 div.matchrow, div.matchitem { | |
| 202 height: 4px; | |
| 203 } | |
| 204 | |
| 205 | |
| 206 table.descriptiontable { | |
| 207 font-size: 85%; | |
| 208 border: 1px solid #97b0c8; | |
| 209 border-spacing: 0; | |
| 210 color: #222222; | |
| 211 line-height: 1.3em; | |
| 212 background-color: white; | |
| 213 } | |
| 214 table.descriptiontable col:first-child { | |
| 215 width: 100%; | |
| 216 } | |
| 217 table.descriptiontable tr:hover { | |
| 218 background-color: #D5DEE3; | |
| 219 } | |
| 220 table.descriptiontable th { | |
| 221 color: #14376C; | |
| 222 font-weight: normal; | |
| 223 background-color: #F0F0F0; | |
| 224 background: linear-gradient(#FFFFFF, #F0F0F0); | |
| 225 border-bottom: 1px solid #D4DFE9; | |
| 226 border-right: 1px solid #CFCFCF; | |
| 227 border-left: 0px solid black; | |
| 228 border-top: 0px solid black; | |
| 229 } | |
| 230 table.descriptiontable td { | |
| 231 overflow: hidden; | |
| 232 text-align: center; | |
| 233 padding: .4em .8em; | |
| 234 } | |
| 235 table.descriptiontable td div { | |
| 236 width: 1em; | |
| 237 overflow: visible; | |
| 238 white-space: nowrap; | |
| 239 text-align: left; | |
| 240 } | |
| 241 | |
| 242 | |
| 243 | |
| 244 .alignments .white { | |
| 245 padding: 1.5em 1em; | |
| 246 } | |
| 247 | |
| 248 .alignment { | |
| 249 border-top: 1px solid black; | |
| 250 padding-left: 1em; | |
| 251 padding-right: 1em; | |
| 252 } | |
| 253 | |
| 254 div.linkheader { | |
| 255 padding-top: .2em; | |
| 256 font-size: 85%; | |
| 257 color: #14376C; | |
| 258 } | |
| 259 div.linkheader a.linkheader { | |
| 260 margin-right: 1em; | |
| 261 } | |
| 262 div.linkheader .right a { | |
| 263 text-decoration: none; | |
| 264 } | |
| 265 | |
| 266 .title .hittitle { | |
| 267 color: #222222; | |
| 268 margin-bottom: .3em; | |
| 269 } | |
| 270 .title .titleinfo { | |
| 271 font-size: 80%; | |
| 272 margin-top: 0; | |
| 273 margin-bottom: .3em; | |
| 274 } | |
| 275 .title .titleinfo .b { | |
| 276 color: #606060; | |
| 277 font-weight: bold; | |
| 278 font-size: 90%; | |
| 279 } | |
| 280 | |
| 281 .moretitles { | |
| 282 margin: 1.2em; | |
| 283 } | |
| 284 .moretitles .titleinfo { | |
| 285 margin: 0; | |
| 286 padding: 0; | |
| 287 } | |
| 288 .moretitles .hittitle { | |
| 289 margin: .4em 0 .2em 0; | |
| 290 padding: 0; | |
| 291 } | |
| 292 | |
| 293 a.showmoretitles { | |
| 294 font-size: 75%; | |
| 295 color: #336699; | |
| 296 font-weight: bold; | |
| 297 margin-top: 0; | |
| 298 } | |
| 299 a.showmoretitles:hover { | |
| 300 } | |
| 301 | |
| 302 .hotspot { | |
| 303 color: #606060; | |
| 304 font-family: verdana, arial, sans-serif; | |
| 305 margin-bottom: 2.5em; | |
| 306 } | |
| 307 | |
| 308 .hotspot p.range { | |
| 309 font-size: 70%; | |
| 310 margin-top: 0; | |
| 311 margin-top: 1em; | |
| 312 margin-bottom: .2em; | |
| 313 } | |
| 314 .hotspot p.range span.range { | |
| 315 font-weight: bold; | |
| 316 } | |
| 317 .hotspot p.range a.range { | |
| 318 margin-left: .5em; | |
| 319 } | |
| 320 | |
| 321 table.hotspotstable { | |
| 322 border-top: 1px solid; | |
| 323 border-bottom: 1px solid; | |
| 324 text-align: left; | |
| 325 border-collapse: collapse; | |
| 326 } | |
| 327 table.hotspotstable th, table.hotspotstable td { | |
| 328 padding: .1em 1em; | |
| 329 } | |
| 330 table.hotspotstable th { | |
| 331 font-size: 70%; | |
| 332 } | |
| 333 table.hotspotstable td { | |
| 334 min-width: 7em; | |
| 335 color: #222222; | |
| 336 font-size: 80%; | |
| 337 } | |
| 338 | |
| 339 pre.alignmentgraphic { | |
| 340 color: #222222; | |
| 341 } | |
| 342 | |
| 343 | |
| 344 </style> | |
| 345 | |
| 346 <script type="text/javascript"> | |
| 347 function toggle_visibility(id) { | |
| 348 var e = document.getElementById(id); | |
| 349 if(e.style.display != 'block') | |
| 350 e.style.display = 'block'; | |
| 351 else | |
| 352 e.style.display = 'none'; | |
| 353 } | |
| 354 </script> | |
| 355 | |
| 356 </head> | |
| 357 | |
| 358 | |
| 359 <body> | |
| 360 <div id=content> | |
| 361 | |
| 362 {% if not blast.BlastOutput_iterations.findall('Iteration') %} | |
| 363 <section class=nodata> | |
| 364 <h1>No data</h1> | |
| 365 <div class=grey> | |
| 366 No matches | |
| 367 </div> | |
| 368 </section> | |
| 369 | |
| 370 {% else %} | |
| 371 | |
| 372 {% if blast.BlastOutput_iterations.findall('Iteration') | length > 1 %} | |
| 373 <section class=index> | |
| 374 <h1>Queries</h1> | |
| 375 | |
| 376 {% for result in blast.BlastOutput_iterations.Iteration %} | |
| 377 <div class=indexentry><a href="#match{{result['Iteration_iter-num']}}"> | |
| 378 {% set hits = result|hits %} | |
| 379 {{result['Iteration_query-ID']}}: {{result['Iteration_query-def']}} | |
| 380 ({{result|len}} letters, {{hits|length}} hits) | |
| 381 </a></div> | |
| 382 {% endfor %} | |
| 383 | |
| 384 </section> | |
| 385 {% endif %} | |
| 386 | |
| 387 {% for result in blast.BlastOutput_iterations.Iteration %} | |
| 388 | |
| 389 <section class=match id=match{{result['Iteration_iter-num']}}> | |
| 390 | |
| 391 <h1>Nucleotide Sequence ({{result|len}} letters)</h1> | |
| 392 | |
| 393 <section class=header> | |
| 394 | |
| 395 <table class=headerdata> | |
| 396 {% for param, value in params %} | |
| 397 <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr> | |
| 398 {% endfor %} | |
| 399 </table> | |
| 400 | |
| 401 </section> | |
| 402 | |
| 403 {% set hits = result|hits %} | |
| 404 {% if not hits %} | |
| 405 <section> | |
| 406 <h2>No Hits</h2> | |
| 407 <div class=grey> | |
| 408 This query did not match anywhere | |
| 409 </div> | |
| 410 </section> | |
| 411 {% else %} | |
| 412 | |
| 413 <section class=graphics> | |
| 414 <h2>Graphic Summary</h2> | |
| 415 | |
| 416 <div class=grey> | |
| 417 <h3 class=centered>Distribution of {{result|length}} Blast Hits on the Query Sequence</h3> | |
| 418 | |
| 419 <div class=defline id=defline{{result['Iteration_iter-num']}}> | |
| 420 Mouse-over to show defline and scores, click to show alignments | |
| 421 </div> | |
| 422 | |
| 423 <div class=graphic> | |
| 424 <h4 class=darkHeader>Color key for alignment scores</h4> | |
| 425 <div class=legend><div class=graphicrow> | |
| 426 <div class=graphicitem style="background-color: {{colors[0]}}"><40</div> | |
| 427 <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div> | |
| 428 <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div> | |
| 429 <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div> | |
| 430 <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div> | |
| 431 </div></div> | |
| 432 <div style="clear: left"></div> | |
| 433 | |
| 434 <div class=tablewrapper> | |
| 435 | |
| 436 <div class=scale> | |
| 437 <div>query:</div> | |
| 438 <div class=graphicrow> | |
| 439 <div> | |
| 440 {% for s in result|queryscale %} | |
| 441 <div class=graphicitem style="width: {{s.width}}%"> | |
| 442 {% if s.width > 3.0 %} | |
| 443 <div>{{s.label}}</div> | |
| 444 {% else %} | |
| 445 <div> </div> | |
| 446 <div class=lastlabel>{{s.label}}</div> | |
| 447 {% endif %} | |
| 448 </div> | |
| 449 {% endfor %} | |
| 450 </div> | |
| 451 </div> | |
| 452 <div style="clear: left"></div> | |
| 453 </div> | |
| 454 | |
| 455 {% for line in result|match_colors %} | |
| 456 <a class=matchresult | |
| 457 href="{{line.link}}" | |
| 458 onmouseover='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="{{line.defline|js_string_escape}}"' | |
| 459 onmouseout='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="Mouse-over to show defline and scores, click to show alignments"' | |
| 460 title="{{line.defline}}"> | |
| 461 <div class="matchrow graphicrow"> | |
| 462 {% for hit in line.colors %} | |
| 463 <div class="matchitem graphicitem" | |
| 464 style="background-color: {{hit[1]}}; width: {{hit[0]}}%"></div> | |
| 465 {% endfor %} | |
| 466 </div> | |
| 467 </a> | |
| 468 | |
| 469 {% endfor %} | |
| 470 </div> | |
| 471 </div> | |
| 472 </div> | |
| 473 </section> | |
| 474 | |
| 475 | |
| 476 | |
| 477 <section class=descriptions> | |
| 478 <h2>Descriptions</h2> | |
| 479 | |
| 480 <div class=grey><div class=white> | |
| 481 <h4 class=darkHeader>Sequences producing significant alignments:</h4> | |
| 482 | |
| 483 <table class=descriptiontable> | |
| 484 <col/><col/><col/><col/><col/><col/><col/> | |
| 485 <tr> | |
| 486 <th>Description</th> | |
| 487 <th>Max score</th> | |
| 488 <th>Total score</th> | |
| 489 <th>Query cover</th> | |
| 490 <th>E value</th> | |
| 491 <th>Ident</th> | |
| 492 <th>Accession</th> | |
| 493 </tr> | |
| 494 {% for hit in result|hit_info %} | |
| 495 <tr> | |
| 496 <td><div><a href="#hit{{hit.link_id}}" | |
| 497 title="{{hit.title}}" | |
| 498 id="description{{hit.link_id}}"> | |
| 499 {{hit.title}} | |
| 500 </a></div></td> | |
| 501 <td>{{hit.maxscore}}</td> | |
| 502 <td>{{hit.totalscore}}</td> | |
| 503 <td>{{hit.cover}}</td> | |
| 504 <td>{{hit.e_value}}</td> | |
| 505 <td>{{hit.ident}}</td> | |
| 506 <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td> | |
| 507 </tr> | |
| 508 {% endfor %} | |
| 509 </table> | |
| 510 | |
| 511 </div></div> | |
| 512 </section> | |
| 513 | |
| 514 | |
| 515 | |
| 516 <section class=alignments> | |
| 517 <h2>Alignments</h2> | |
| 518 | |
| 519 <div class=grey><div class=white> | |
| 520 {% for hit in hits %} | |
| 521 <div class=alignment id=hit{{hit.Hit_num}}> | |
| 522 | |
| 523 <div class=linkheader> | |
| 524 <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div> | |
| 525 <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a> | |
| 526 <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a> | |
| 527 </div> | |
| 528 | |
| 529 <div class=title> | |
| 530 <p class=hittitle>{{hit|firsttitle}}</p> | |
| 531 <p class=titleinfo> | |
| 532 <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a> | |
| 533 <span class=b>Length:</span> {{hit.Hit_len}} | |
| 534 <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}} | |
| 535 </p> | |
| 536 </div> | |
| 537 | |
| 538 {% if hit|othertitles|length %} | |
| 539 <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num|js_string_escape}}'); return false;" href=''> | |
| 540 See {{hit|othertitles|length}} more title(s) | |
| 541 </a> | |
| 542 | |
| 543 <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none"> | |
| 544 {% for title in hit|othertitles %} | |
| 545 <div class=title> | |
| 546 <p class=hittitle>{{title.title}}</p> | |
| 547 <p class=titleinfo> | |
| 548 <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a> | |
| 549 </p> | |
| 550 </div> | |
| 551 {% endfor %} | |
| 552 </div> | |
| 553 {% endif %} | |
| 554 | |
| 555 {% for hsp in hit.Hit_hsps.Hsp %} | |
| 556 <div class=hotspot> | |
| 557 <p class=range> | |
| 558 <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span> | |
| 559 <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a> | |
| 560 <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a> | |
| 561 </p> | |
| 562 | |
| 563 <table class=hotspotstable> | |
| 564 <tr> | |
| 565 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> | |
| 566 </tr> | |
| 567 <tr> | |
| 568 <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td> | |
| 569 <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td> | |
| 570 <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{ | |
| 571 (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td> | |
| 572 <td>{{ hsp.Hsp_gaps }}/{{ hsp|len | |
| 573 }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td> | |
| 574 <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td> | |
| 575 </tr> | |
| 576 </table> | |
| 577 | |
| 578 <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre> | |
| 579 </div> | |
| 580 {% endfor %} | |
| 581 | |
| 582 </div> | |
| 583 | |
| 584 {% endfor %} | |
| 585 </div></div> | |
| 586 </section> | |
| 587 {% endif %} | |
| 588 | |
| 589 {% endfor %} | |
| 590 {% endif %} | |
| 591 </div> | |
| 592 </body> | |
| 593 </html> | |
| 594 | |
| 595 {# | |
| 596 Local Variables: | |
| 597 tab-width: 2 | |
| 598 indent-tabs-mode: nil | |
| 599 End: | |
| 600 #} |