Mercurial > repos > jankanis > blast2html
annotate test-data/blast xml example2.html @ 120:2729c2326235
Fix for Rikilt issue 13
Hit e-value and identity% should be taken from the hsp with the highest
bit score. Previously each of these values was calculated independently.
Also use arrays for cover calculation instead of python lists and
refactor the hit_info() code a bit.
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Thu, 31 Jul 2014 16:14:36 +0200 |
| parents | 4f0ed3b5ae46 |
| children |
| rev | line source |
|---|---|
| 32 | 1 <!DOCTYPE html> |
| 2 <html> | |
| 3 <head> | |
| 4 <meta charset="UTF-8"> | |
|
33
3bb5da68305e
add test update script, add url to github page
Jan Kanis <jan.code@jankanis.nl>
parents:
32
diff
changeset
|
5 <meta name=generator content="blast2html; see https://github.com/thehyve/blast2html/"> |
| 32 | 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 /* Galaxy with html sanitization enabled strips the header of this html page. If so, show the user a warning.*/ | |
| 24 #strip_html_warning { | |
| 25 display: none; | |
| 26 } | |
| 27 | |
| 28 #content { | |
| 29 margin: 0 2em; | |
| 30 padding: 0.5em; | |
| 31 border: 1px solid #888888; | |
| 32 background-color: #d3dff5; | |
| 33 } | |
| 34 | |
| 35 h1, h2, h3, h4, h5, h6 { | |
| 36 color: #2A6979; | |
| 37 font-family: arial,verdana,sans-serif; | |
| 38 letter-spacing: -1px; | |
| 39 margin: 1.2em 0 0.3em; | |
| 40 } | |
| 41 | |
| 42 h1 { | |
| 114 | 43 font-size: 200%; |
| 44 } | |
| 45 | |
| 46 h2 { | |
| 47 font-size: 150%; | |
| 48 } | |
| 49 | |
| 50 h1, h2 { | |
| 32 | 51 border-bottom: 1px solid #CCCCCC; |
| 52 padding-bottom: 0.1em; | |
| 53 } | |
| 54 | |
| 114 | 55 h3 { |
| 32 | 56 font-size: 120%; |
| 57 font-weight: bold; | |
| 58 } | |
| 59 | |
| 114 | 60 h5.darkHeader { |
| 32 | 61 color: #4D4D4D; |
| 62 letter-spacing: 0; | |
| 63 font-weight: bold; | |
| 114 | 64 font-size: 108%; |
| 32 | 65 } |
| 66 | |
| 67 #nodata { | |
| 68 font-weight: bold; | |
| 69 } | |
| 70 | |
| 71 .index { | |
| 72 margin-bottom: 3em; | |
| 73 } | |
| 74 .index div.indexentry { | |
| 75 margin: 1.2em 1.6em; | |
| 76 font-weight: bold; | |
| 77 font-size: 100%; | |
| 78 } | |
| 79 | |
| 80 .headerdata { | |
| 81 font-size: 90%; | |
| 82 } | |
| 83 .headerdata .param { | |
| 84 font-weight: bold; | |
| 85 text-align: right; | |
| 86 padding: 0 1em; | |
| 87 } | |
| 88 | |
| 89 .grey { | |
| 90 background-color: #eeeeee; | |
| 91 border: 1px solid #cccccc; | |
| 92 padding: 1em; | |
| 93 } | |
| 94 | |
| 95 .white { | |
| 96 background-color: white; | |
| 97 border: 1px solid #cccccc; | |
| 98 padding: 1.5em 2%; | |
| 99 } | |
| 100 | |
| 101 .graphicrow { | |
| 102 clear: left; | |
| 103 width: 100%; | |
| 104 } | |
| 105 | |
| 106 .graphicitem { | |
| 107 float: left; | |
| 108 } | |
| 109 | |
| 110 | |
| 111 | |
| 112 .graphics .grey { | |
| 113 text-align: center; | |
| 114 } | |
| 115 | |
| 116 .graphic { | |
| 117 background-color: white; | |
| 118 border: 2px solid black; | |
| 119 padding: 1.5em; | |
| 120 margin: auto; | |
| 121 } | |
| 122 | |
| 123 .centered, .defline, div.legend, div.tablewrapper { | |
| 124 margin-left: auto; | |
| 125 margin-right: auto; | |
| 126 } | |
| 127 | |
| 128 .defline { | |
| 129 background-color: white; | |
| 130 border: 1px solid black; | |
| 131 margin: .5em auto; | |
| 132 padding-left: .2em; | |
| 133 padding-right: .2em; | |
| 134 max-width: 50em; | |
| 135 text-align: left; | |
| 136 height: 2.8em; | |
| 59 | 137 overflow: hidden; |
| 32 | 138 } |
| 139 | |
| 140 div.legend { | |
| 141 max-width: 40em; | |
| 142 } | |
| 143 div.legend div { | |
| 144 width: 100%; | |
| 145 color: white; | |
| 146 font-weight: bold; | |
| 147 border-spacing: 0; | |
| 148 } | |
| 149 div.legend div .graphicitem { | |
| 150 width: 20%; | |
| 151 padding: 0; | |
| 152 margin: 0; | |
| 153 border: none; | |
| 154 } | |
| 155 | |
| 156 div.tablewrapper { | |
| 157 width: 50%; | |
| 158 min-width: 60em; | |
| 159 } | |
| 160 | |
| 161 /* For small widths we give the graphic 100% */ | |
| 162 @media (max-width: 72.5em) { | |
| 163 div.tablewrapper { | |
| 164 width: 100%; | |
| 165 min-width: 0px; | |
| 166 } | |
| 167 } | |
| 168 | |
| 169 .scale { | |
| 170 width: 100%; | |
| 171 margin: .5em 0; | |
| 172 font-weight: bold; | |
| 173 } | |
| 174 .scale div { | |
| 175 color: red; | |
| 176 text-align: left; | |
| 177 } | |
| 178 .scale .graphicrow { | |
| 179 margin: .5em 0 .5em 0; | |
| 180 color: white; | |
| 181 } | |
| 182 .scale .graphicitem { | |
| 183 position: relative; | |
| 184 } | |
| 185 .scale .graphicitem div { | |
| 186 margin: 0 1px; | |
| 187 padding: 0 2px; | |
| 188 text-align: right; | |
| 189 background-color: red; | |
| 190 color: white; | |
| 191 } | |
| 192 .scale .graphicitem:first-child div { | |
| 193 margin-left: 0px; | |
| 194 } | |
| 195 .scale .graphicitem:last-child div { | |
| 196 margin-right: 0px; | |
| 197 } | |
| 198 .scale .graphicitem .lastlabel { | |
| 199 position: absolute; | |
| 200 top: 0px; | |
| 201 left: 100%; | |
| 202 background-color: transparent; | |
| 203 color: red; | |
| 204 } | |
| 205 | |
| 206 a.matchresult { | |
| 207 display: block; | |
| 208 margin: 0; | |
| 209 padding: 0; | |
| 210 } | |
| 211 div.matchrow { | |
| 212 margin-top: 4px; | |
| 213 } | |
| 214 div.matchrow, div.matchitem { | |
| 215 height: 4px; | |
| 216 } | |
| 217 | |
| 218 | |
| 219 table.descriptiontable { | |
| 220 font-size: 85%; | |
| 221 border: 1px solid #97b0c8; | |
| 222 border-spacing: 0; | |
| 223 color: #222222; | |
| 224 line-height: 1.3em; | |
| 225 background-color: white; | |
| 226 } | |
| 227 table.descriptiontable col:first-child { | |
| 228 width: 100%; | |
| 229 } | |
| 230 table.descriptiontable tr:hover { | |
| 231 background-color: #D5DEE3; | |
| 232 } | |
| 233 table.descriptiontable th { | |
| 234 color: #14376C; | |
| 235 font-weight: normal; | |
| 236 background-color: #F0F0F0; | |
| 237 background: linear-gradient(#FFFFFF, #F0F0F0); | |
| 238 border-bottom: 1px solid #D4DFE9; | |
| 239 border-right: 1px solid #CFCFCF; | |
| 240 border-left: 0px solid black; | |
| 241 border-top: 0px solid black; | |
| 242 } | |
| 243 table.descriptiontable td { | |
| 244 overflow: hidden; | |
| 245 text-align: center; | |
| 246 padding: .4em .8em; | |
| 247 } | |
| 248 table.descriptiontable td div { | |
| 249 width: 1em; | |
| 250 overflow: visible; | |
| 251 white-space: nowrap; | |
| 252 text-align: left; | |
| 253 } | |
| 254 | |
| 255 | |
| 256 | |
| 257 .alignments .white { | |
| 258 padding: 1.5em 1em; | |
| 259 } | |
| 260 | |
| 261 .alignment { | |
| 262 border-top: 1px solid black; | |
| 263 padding-left: 1em; | |
| 264 padding-right: 1em; | |
| 265 } | |
| 266 | |
| 267 div.linkheader { | |
| 268 padding-top: .2em; | |
| 269 font-size: 85%; | |
| 270 color: #14376C; | |
| 271 } | |
| 272 div.linkheader a.linkheader { | |
| 273 margin-right: 1em; | |
| 274 } | |
| 275 div.linkheader .right a { | |
| 276 text-decoration: none; | |
| 277 } | |
| 278 | |
| 279 .title .hittitle { | |
| 280 color: #222222; | |
| 281 margin-bottom: .3em; | |
| 282 } | |
| 283 .title .titleinfo { | |
| 284 font-size: 80%; | |
| 285 margin-top: 0; | |
| 286 margin-bottom: .3em; | |
| 287 } | |
| 288 .title .titleinfo .b { | |
| 289 color: #606060; | |
| 290 font-weight: bold; | |
| 291 font-size: 90%; | |
| 292 } | |
| 293 | |
| 294 .moretitles { | |
| 295 margin: 1.2em; | |
| 296 } | |
| 297 .moretitles .titleinfo { | |
| 298 margin: 0; | |
| 299 padding: 0; | |
| 300 } | |
| 301 .moretitles .hittitle { | |
| 302 margin: .4em 0 .2em 0; | |
| 303 padding: 0; | |
| 304 } | |
| 305 | |
| 306 a.showmoretitles { | |
| 307 font-size: 75%; | |
| 308 color: #336699; | |
| 309 font-weight: bold; | |
| 310 margin-top: 0; | |
| 311 } | |
| 312 a.showmoretitles:hover { | |
| 313 } | |
| 314 | |
| 315 .hotspot { | |
| 316 color: #606060; | |
| 317 font-family: verdana, arial, sans-serif; | |
| 318 margin-bottom: 2.5em; | |
| 319 } | |
| 320 | |
| 321 .hotspot p.range { | |
| 322 font-size: 70%; | |
| 323 margin-top: 0; | |
| 324 margin-top: 1em; | |
| 325 margin-bottom: .2em; | |
| 326 } | |
| 327 .hotspot p.range span.range { | |
| 328 font-weight: bold; | |
| 329 } | |
| 330 .hotspot p.range a.range { | |
| 331 margin-left: .5em; | |
| 332 } | |
| 333 | |
| 334 table.hotspotstable { | |
| 335 border-top: 1px solid; | |
| 336 border-bottom: 1px solid; | |
| 337 text-align: left; | |
| 338 border-collapse: collapse; | |
| 339 } | |
| 340 table.hotspotstable th, table.hotspotstable td { | |
| 341 padding: .1em 1em; | |
| 342 } | |
| 343 table.hotspotstable th { | |
| 344 font-size: 70%; | |
| 345 } | |
| 346 table.hotspotstable td { | |
| 347 min-width: 7em; | |
| 348 color: #222222; | |
| 349 font-size: 80%; | |
| 350 } | |
| 351 | |
| 352 pre.alignmentgraphic { | |
| 353 color: #222222; | |
| 354 } | |
| 355 | |
| 356 footer { | |
| 357 text-align: center; | |
| 358 color: #cccccc; | |
| 359 font-size: 70%; | |
| 360 margin-top: 1em; | |
| 361 } | |
| 362 footer :link { | |
| 363 color: #5588cc; | |
| 364 } | |
| 365 | |
| 366 </style> | |
| 367 | |
| 368 <script type="text/javascript"> | |
| 369 function toggle_visibility(id) { | |
| 370 var e = document.getElementById(id); | |
| 371 if(e.style.display != 'block') | |
| 372 e.style.display = 'block'; | |
| 373 else | |
| 374 e.style.display = 'none'; | |
| 375 } | |
| 376 </script> | |
| 377 | |
| 378 </head> | |
| 379 | |
| 380 | |
| 381 <body> | |
| 382 | |
| 383 <div id="strip_html_warning"> | |
| 384 <!-- This div should be hidden by the header css block. Galaxy | |
| 385 strips all css, breaking this page but making this warning | |
| 386 visible. This warning contains some ugly old skool tabular html | |
| 387 layout that is not stripped. --> | |
| 388 <table bgcolor="#FFE5C9"><tr><td><font color="red"><b> | |
| 389 <font size=5><center>This html page seems to have been stripped by Galaxy.</center></font> | |
| 390 Disable Galaxy's html sanitization feature to view the full page (see <font face=monospace>sanitize_all_html</font> in your galaxy's universe_wsgi.ini), or download this page instead of viewing it in Galaxy. | |
| 391 </b></font></td></tr></table> | |
| 392 </div> | |
| 393 | |
| 394 <div id=content> | |
| 395 | |
| 114 | 396 <section class=header> |
| 397 | |
| 398 <h1>Nucleotide Blast results</h1> | |
| 399 | |
| 400 <table class=headerdata> | |
| 401 <tr><td class=param>Program:</td><td>BLASTN 2.2.28+</td></tr> | |
| 402 <tr><td class=param>Database:</td><td>/share/BlastDB/nt</td></tr> | |
| 403 </table> | |
| 404 | |
| 405 </section> | |
| 406 | |
| 32 | 407 |
| 408 | |
| 409 | |
| 410 <section class=match id=match1> | |
| 411 | |
| 114 | 412 <h2>Nucleotide Sequence (16 letters)</h2> |
| 32 | 413 |
| 414 <section class=header> | |
| 415 | |
| 416 <table class=headerdata> | |
| 114 | 417 <tr><td class=param>Query number:</td><td>1</td></tr> |
| 32 | 418 <tr><td class=param>Query ID:</td><td>Query_1</td></tr> |
| 114 | 419 <tr><td class=param>Definition line:</td><td>No definition line</td></tr> |
| 420 <tr><td class=param>Length:</td><td>16</td></tr> | |
| 32 | 421 </table> |
| 422 | |
| 423 </section> | |
| 424 | |
| 425 <section> | |
| 114 | 426 <h3>No Hits</h3> |
| 32 | 427 <div class=grey> |
| 428 <table class=headerdata> | |
| 429 <tr><td class=param>Message:</td><td>No hits found</td></tr> | |
| 430 </table> | |
| 431 </div> | |
| 432 </section> | |
| 433 </section> | |
| 434 | |
| 435 </div> | |
| 436 | |
| 437 <footer> | |
|
33
3bb5da68305e
add test update script, add url to github page
Jan Kanis <jan.code@jankanis.nl>
parents:
32
diff
changeset
|
438 This page was generated by <a href="https://github.com/thehyve/blast2html/">blast2html</a>. |
| 32 | 439 </footer> |
| 440 </body> | |
| 441 </html> | |
| 442 |