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201 <li class="edge-item-fix"><a href="/explore" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Explore">Explore GitHub <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li>
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202 </ul>
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203
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204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn & contribute</h4>
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205 <ul class="list-style-none mb-3">
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206 <li class="edge-item-fix"><a href="/topics" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Topics">Topics</a></li>
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207 <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li>
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208 <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li>
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209 <li class="edge-item-fix"><a href="https://lab.github.com/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Learning lab">Learning Lab</a></li>
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210 <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li>
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211 </ul>
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212
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213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4>
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214 <ul class="list-style-none mb-0">
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215 <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li>
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216 <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li>
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217 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li>
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218 </ul>
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219 </div>
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220 </details>
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221 </li>
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222
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223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
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224 <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a>
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225 </li>
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226
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227 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
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228 <details class="HeaderMenu-details details-overlay details-reset width-full">
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229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
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230 Pricing
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231 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative">
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232 <path d="M1,1l6.2,6L13,1"></path>
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233 </svg>
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234 </summary>
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235
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236 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
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237 <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a>
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238
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239 <ul class="list-style-none mb-3">
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240 <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li>
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241 <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li>
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242 </ul>
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243
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244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
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245 <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li>
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246 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li>
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247 </ul>
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248 </div>
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249 </details>
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250 </li>
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251 </ul>
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252 </nav>
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253
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254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left">
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255 <div class="d-lg-flex mb-3 mb-lg-0">
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256 <div class="header-search flex-self-stretch flex-lg-self-auto mr-0 mr-lg-3 mb-3 mb-lg-0 scoped-search site-scoped-search js-site-search position-relative js-jump-to"
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257 role="combobox"
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258 aria-owns="jump-to-results"
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259 aria-label="Search or jump to"
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260 aria-haspopup="listbox"
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261 aria-expanded="false"
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262 >
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263 <div class="position-relative">
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264 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="139730674" data-scoped-search-url="/johnheap/VAPPER-Galaxy/search" data-unscoped-search-url="/search" action="/johnheap/VAPPER-Galaxy/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" />
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265 <label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container">
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266 <input type="text"
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267 class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable"
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268 data-hotkey="s,/"
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269 name="q"
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270 value=""
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271 placeholder="Search"
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272 data-unscoped-placeholder="Search GitHub"
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273 data-scoped-placeholder="Search"
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274 autocapitalize="off"
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275 aria-autocomplete="list"
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276 aria-controls="jump-to-results"
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277 aria-label="Search"
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278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=5MzQ1RlnTKXgRukE3fvG6coUoC2g7caP2Y7AEhL1aj7jsO5luTpWqHOrjoWoNlAo1ormLPudsQBeevTJJMYJwQ=="
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279 spellcheck="false"
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280 autocomplete="off"
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281 >
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282 <input type="hidden" class="js-site-search-type-field" name="type" >
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283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
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284
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|
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285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
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286
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287 <ul class="d-none js-jump-to-suggestions-template-container">
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288
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289
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290 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option">
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291 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
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292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
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293 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
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294 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
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295 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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296 </div>
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297
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298 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
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299
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|
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300 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
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|
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301 </div>
|
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302
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|
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303 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
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304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
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305 In this repository
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306 </span>
|
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307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
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308 All GitHub
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309 </span>
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310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
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311 </div>
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312
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|
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313 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
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314 Jump to
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315 <span class="d-inline-block ml-1 v-align-middle">↵</span>
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316 </div>
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317 </a>
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318 </li>
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319
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320 </ul>
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321
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322 <ul class="d-none js-jump-to-no-results-template-container">
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323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2">
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324 <span class="text-gray">No suggested jump to results</span>
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325 </li>
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326 </ul>
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327
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328 <ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container">
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|
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329
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|
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330
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331 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option">
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332 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
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333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
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334 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
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335 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
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336 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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337 </div>
|
|
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338
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|
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339 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
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|
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340
|
|
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341 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
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|
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342 </div>
|
|
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343
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|
|
344 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
|
|
|
345 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
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|
|
346 In this repository
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347 </span>
|
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|
348 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
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349 All GitHub
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350 </span>
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351 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
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352 </div>
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353
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354 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
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355 Jump to
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356 <span class="d-inline-block ml-1 v-align-middle">↵</span>
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357 </div>
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358 </a>
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359 </li>
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360
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361
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362
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363 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option">
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|
|
364 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
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|
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365 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
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366 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
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367 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
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368 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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369 </div>
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370
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371 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
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372
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373 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
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|
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374 </div>
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375
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|
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376 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
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377 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
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378 In this repository
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379 </span>
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380 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
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381 All GitHub
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382 </span>
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383 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
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384 </div>
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385
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386 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
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387 Jump to
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405 </a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"99F4:18E6:6FD3A:CCBBE:5CF562F5","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Vap.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="61d34ac29eda53a9af41882fb756e16915c4f2c290c4b6305a2d6e690cf24bbf" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
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436 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav pt-0 pt-lg-4 ">
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604 <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/prompt_dismissals/signup" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="✓" /><input type="hidden" name="_method" value="put" /><input type="hidden" name="authenticity_token" value="01xCvegbK4lYlEbK5GWZDSH9FJauuJqGMpPpkxSUd6hDt3L8B3yee+h/iSIIdplnCf6cn0xKaAqoHNilP5KQdA==" />
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605 <button type="submit" class="position-absolute top-0 right-0 btn-link link-gray" data-ga-click="(Logged out) Sign up prompt, clicked Dismiss, text:dismiss">
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606 Dismiss
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607 </button>
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608 </form> <h3 class="pt-2">Join GitHub today</h3>
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609 <p class="col-6 mx-auto">GitHub is home to over 36 million developers working together to host and review code, manage projects, and build software together.</p>
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610 <a class="btn btn-primary" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"files signup prompt","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"99F4:18E6:6FD3A:CCBBE:5CF562F5","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Vap.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="4fb80a26df9a3a549b2b9672e4ab87e6fd8d2143a09bd70bf44f9e9a8de20937" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up" href="/join?source=prompt-blob-show">Sign up</a>
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611 </div>
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612 </div>
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613 </div>
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614
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615
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616 <div class="d-flex flex-items-start flex-shrink-0 mb-2 flex-column flex-md-row">
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617 <span class="d-flex flex-justify-between width-full width-md-auto">
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618
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619 <details class="details-reset details-overlay select-menu branch-select-menu hx_rsm" id="branch-select-menu">
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620 <summary class="btn btn-sm select-menu-button css-truncate"
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621 data-hotkey="w"
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622
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623 title="Switch branches or tags">
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624 <i>Branch:</i>
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625 <span class="css-truncate-target">master</span>
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626 </summary>
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627
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628 <details-menu class="select-menu-modal hx_rsm-modal position-absolute" style="z-index: 99;" src="/johnheap/VAPPER-Galaxy/ref-list/master/Vap.py?source_action=show&source_controller=blob" preload>
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630 <svg height="32" class="octicon octicon-octoface" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M14.7 5.34c.13-.32.55-1.59-.13-3.31 0 0-1.05-.33-3.44 1.3-1-.28-2.07-.32-3.13-.32s-2.13.04-3.13.32c-2.39-1.64-3.44-1.3-3.44-1.3-.68 1.72-.26 2.99-.13 3.31C.49 6.21 0 7.33 0 8.69 0 13.84 3.33 15 7.98 15S16 13.84 16 8.69c0-1.36-.49-2.48-1.3-3.35zM8 14.02c-3.3 0-5.98-.15-5.98-3.35 0-.76.38-1.48 1.02-2.07 1.07-.98 2.9-.46 4.96-.46 2.07 0 3.88-.52 4.96.46.65.59 1.02 1.3 1.02 2.07 0 3.19-2.68 3.35-5.98 3.35zM5.49 9.01c-.66 0-1.2.8-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.54-1.78-1.2-1.78zm5.02 0c-.66 0-1.2.79-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.53-1.78-1.2-1.78z"/></svg>
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631 </include-fragment>
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632 </details-menu>
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633 </details>
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634
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635 <div class="BtnGroup flex-shrink-0 d-md-none">
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636 <a href="/johnheap/VAPPER-Galaxy/find/master"
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637 class="js-pjax-capture-input btn btn-sm BtnGroup-item"
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638 data-pjax
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639 data-hotkey="t">
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640 Find file
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641 </a>
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642 <clipboard-copy value="Vap.py" class="btn btn-sm BtnGroup-item">
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643 Copy path
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644 </clipboard-copy>
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645 </div>
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646 </span>
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647 <h2 id="blob-path" class="breadcrumb flex-auto min-width-0 text-normal flex-md-self-center ml-md-2 mr-md-3 my-2 my-md-0">
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648 <span class="js-repo-root text-bold"><span class="js-path-segment"><a data-pjax="true" href="/johnheap/VAPPER-Galaxy"><span>VAPPER-Galaxy</span></a></span></span><span class="separator">/</span><strong class="final-path">Vap.py</strong>
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649 </h2>
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650
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651 <div class="BtnGroup flex-shrink-0 d-none d-md-inline-block">
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652 <a href="/johnheap/VAPPER-Galaxy/find/master"
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653 class="js-pjax-capture-input btn btn-sm BtnGroup-item"
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654 data-pjax
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655 data-hotkey="t">
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656 Find file
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657 </a>
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658 <clipboard-copy value="Vap.py" class="btn btn-sm BtnGroup-item">
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659 Copy path
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660 </clipboard-copy>
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661 </div>
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662 </div>
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663
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664
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665
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666 <include-fragment src="/johnheap/VAPPER-Galaxy/contributors/master/Vap.py" class="Box Box--condensed commit-loader">
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667 <div class="Box-body bg-blue-light f6">
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668 Fetching contributors…
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669 </div>
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670
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671 <div class="Box-body d-flex flex-items-center" >
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672 <img alt="" class="loader-loading mr-2" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" />
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673 <span class="text-red h6 loader-error">Cannot retrieve contributors at this time</span>
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674 </div>
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675 </include-fragment>
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676
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677
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678
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679
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680
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681 <div class="Box mt-3 position-relative">
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682
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683 <div class="Box-header py-2 d-flex flex-column flex-shrink-0 flex-md-row flex-md-items-center">
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684
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685 <div class="text-mono f6 flex-auto pr-3 flex-order-2 flex-md-order-1 mt-2 mt-md-0">
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686 81 lines (72 sloc)
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687 <span class="file-info-divider"></span>
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688 3.04 KB
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689 </div>
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690
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691 <div class="d-flex py-1 py-md-0 flex-auto flex-order-1 flex-md-order-2 flex-sm-grow-0 flex-justify-between">
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692
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693 <div class="BtnGroup">
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694 <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/raw/master/Vap.py">Raw</a>
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695 <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/johnheap/VAPPER-Galaxy/blame/master/Vap.py">Blame</a>
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696 <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/Vap.py">History</a>
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697 </div>
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698
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699
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700 <div>
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701
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702 <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw"
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703 aria-label="You must be signed in to make or propose changes">
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704 <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg>
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705 </button>
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706 <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw"
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707 aria-label="You must be signed in to make or propose changes">
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708 <svg class="octicon octicon-trashcan" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg>
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709 </button>
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710 </div>
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711 </div>
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712 </div>
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713
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714
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715
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716 <div itemprop="text" class="Box-body p-0 blob-wrapper data type-python ">
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717
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718 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
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719 <tr>
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720 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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721 <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">"""</span></span></td>
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722 </tr>
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723 <tr>
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724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td>
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726 </tr>
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727 <tr>
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728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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729 <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author: John Heap, Computational Biology Facility, UoL</span></td>
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730 </tr>
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731 <tr>
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732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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733 <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td>
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734 </tr>
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735 <tr>
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736 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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737 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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738 </tr>
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739 <tr>
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740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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741 <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the "License");</span></td>
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742 </tr>
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743 <tr>
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744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
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745 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td>
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746 </tr>
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747 <tr>
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748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
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749 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td>
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750 </tr>
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751 <tr>
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752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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753 <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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754 </tr>
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755 <tr>
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756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
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757 <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td>
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758 </tr>
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759 <tr>
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760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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762 </tr>
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763 <tr>
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764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
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765 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td>
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766 </tr>
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767 <tr>
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768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
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769 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td>
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770 </tr>
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771 <tr>
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772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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773 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td>
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774 </tr>
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775 <tr>
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776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
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777 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td>
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778 </tr>
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779 <tr>
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780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
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781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td>
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782 </tr>
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783 <tr>
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784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
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785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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786 </tr>
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787 <tr>
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788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
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789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td>
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790 </tr>
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791 <tr>
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792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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793 <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import subprocess</span></td>
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794 </tr>
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795 <tr>
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796 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
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797 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import re</span></td>
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798 </tr>
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799 <tr>
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800 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
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801 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td>
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802 </tr>
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803 <tr>
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804 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
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805 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
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806 </tr>
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807 <tr>
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808 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
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809 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import pandas as pd</span></td>
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810 </tr>
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811 <tr>
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812 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
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813 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import numpy as np</span></td>
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814 </tr>
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815 <tr>
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816 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
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817 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import seaborn as sns</span></td>
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818 </tr>
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819 <tr>
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820 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
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821 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import matplotlib.pyplot as plt</span></td>
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822 </tr>
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823 <tr>
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824 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
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825 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>from matplotlib.mlab import PCA</span></td>
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826 </tr>
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827 <tr>
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828 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
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829 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_G</td>
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830 </tr>
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831 <tr>
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832 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
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833 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_T</td>
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834 </tr>
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835 <tr>
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836 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
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837 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V</td>
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|
838 </tr>
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839 <tr>
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|
840 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
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841 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V_T</td>
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|
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842 </tr>
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843 <tr>
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844 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
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845 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> argparse</td>
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846 </tr>
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847 <tr>
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848 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
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849 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>Entry .sort out the arguments</span></td>
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850 </tr>
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|
851 <tr>
|
|
|
852 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
|
|
|
853 <td id="LC34" class="blob-code blob-code-inner js-file-line">
|
|
|
854 </td>
|
|
|
855 </tr>
|
|
|
856 <tr>
|
|
|
857 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
|
|
|
858 <td id="LC35" class="blob-code blob-code-inner js-file-line">pdfExport <span class="pl-k">=</span> <span class="pl-c1">False</span></td>
|
|
|
859 </tr>
|
|
|
860 <tr>
|
|
|
861 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
|
|
|
862 <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.')</span></td>
|
|
|
863 </tr>
|
|
|
864 <tr>
|
|
|
865 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
|
|
|
866 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('name')</span></td>
|
|
|
867 </tr>
|
|
|
868 <tr>
|
|
|
869 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
|
|
|
870 <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway")</span></td>
|
|
|
871 </tr>
|
|
|
872 <tr>
|
|
|
873 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
|
|
|
874 <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory")</span></td>
|
|
|
875 </tr>
|
|
|
876 <tr>
|
|
|
877 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
|
|
|
878 <td id="LC40" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('strain')</span></td>
|
|
|
879 </tr>
|
|
|
880 <tr>
|
|
|
881 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
|
|
|
882 <td id="LC41" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('Forward_Read_File')</span></td>
|
|
|
883 </tr>
|
|
|
884 <tr>
|
|
|
885 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
|
|
|
886 <td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('Reverse_Read_File')</span></td>
|
|
|
887 </tr>
|
|
|
888 <tr>
|
|
|
889 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
|
|
|
890 <td id="LC43" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('htmlfile')</span></td>
|
|
|
891 </tr>
|
|
|
892 <tr>
|
|
|
893 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
|
|
|
894 <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('htmlresource')</span></td>
|
|
|
895 </tr>
|
|
|
896 <tr>
|
|
|
897 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
|
|
|
898 <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('heatmapFile')</span></td>
|
|
|
899 </tr>
|
|
|
900 <tr>
|
|
|
901 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
|
|
|
902 <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('PCAFile')</span></td>
|
|
|
903 </tr>
|
|
|
904 <tr>
|
|
|
905 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
|
|
|
906 <td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('devheatmapFile')</span></td>
|
|
|
907 </tr>
|
|
|
908 <tr>
|
|
|
909 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
|
|
|
910 <td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>args = parser.parse_args()</span></td>
|
|
|
911 </tr>
|
|
|
912 <tr>
|
|
|
913 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
|
|
|
914 <td id="LC49" class="blob-code blob-code-inner js-file-line">
|
|
|
915 </td>
|
|
|
916 </tr>
|
|
|
917 <tr>
|
|
|
918 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
|
|
|
919 <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>we have numerous parameters....</span></td>
|
|
|
920 </tr>
|
|
|
921 <tr>
|
|
|
922 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
|
|
|
923 <td id="LC51" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>hard code it for differnt types?</span></td>
|
|
|
924 </tr>
|
|
|
925 <tr>
|
|
|
926 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
|
|
|
927 <td id="LC52" class="blob-code blob-code-inner js-file-line">
|
|
|
928 </td>
|
|
|
929 </tr>
|
|
|
930 <tr>
|
|
|
931 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
|
|
|
932 <td id="LC53" class="blob-code blob-code-inner js-file-line">
|
|
|
933 </td>
|
|
|
934 </tr>
|
|
|
935 <tr>
|
|
|
936 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
|
|
|
937 <td id="LC54" class="blob-code blob-code-inner js-file-line">arguments <span class="pl-k">=</span> sys.argv</td>
|
|
|
938 </tr>
|
|
|
939 <tr>
|
|
|
940 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
|
|
|
941 <td id="LC55" class="blob-code blob-code-inner js-file-line">htmldir <span class="pl-k">=</span> arguments[<span class="pl-c1">len</span>(arguments)<span class="pl-k">-</span><span class="pl-c1">1</span>] <span class="pl-c"><span class="pl-c">#</span>last argument is always html_resource</span></td>
|
|
|
942 </tr>
|
|
|
943 <tr>
|
|
|
944 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
|
|
|
945 <td id="LC56" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-k">not</span> os.path.exists(htmldir):</td>
|
|
|
946 </tr>
|
|
|
947 <tr>
|
|
|
948 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
|
|
|
949 <td id="LC57" class="blob-code blob-code-inner js-file-line"> os.mkdir(htmldir)</td>
|
|
|
950 </tr>
|
|
|
951 <tr>
|
|
|
952 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
|
|
|
953 <td id="LC58" class="blob-code blob-code-inner js-file-line">
|
|
|
954 </td>
|
|
|
955 </tr>
|
|
|
956 <tr>
|
|
|
957 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
|
|
|
958 <td id="LC59" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>g_assemble<span class="pl-pds">'</span></span>:</td>
|
|
|
959 </tr>
|
|
|
960 <tr>
|
|
|
961 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
|
|
|
962 <td id="LC60" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>kmers<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>,<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>:<span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>:<span class="pl-c1">8</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">9</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">10</span>}</td>
|
|
|
963 </tr>
|
|
|
964 <tr>
|
|
|
965 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
|
|
|
966 <td id="LC61" class="blob-code blob-code-inner js-file-line"> Tryp_G.assemble(arguments,argdict)</td>
|
|
|
967 </tr>
|
|
|
968 <tr>
|
|
|
969 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
|
|
|
970 <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>g_contigs<span class="pl-pds">'</span></span>:</td>
|
|
|
971 </tr>
|
|
|
972 <tr>
|
|
|
973 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
|
|
|
974 <td id="LC63" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>}</td>
|
|
|
975 </tr>
|
|
|
976 <tr>
|
|
|
977 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
|
|
|
978 <td id="LC64" class="blob-code blob-code-inner js-file-line"> Tryp_G.contigs(arguments,argdict)</td>
|
|
|
979 </tr>
|
|
|
980 <tr>
|
|
|
981 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
|
|
|
982 <td id="LC65" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>transcipt<span class="pl-pds">'</span></span>:</td>
|
|
|
983 </tr>
|
|
|
984 <tr>
|
|
|
985 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
|
|
|
986 <td id="LC66" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>: <span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>: <span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>: <span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>: <span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>: <span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>: <span class="pl-c1">8</span>}</td>
|
|
|
987 </tr>
|
|
|
988 <tr>
|
|
|
989 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
|
|
|
990 <td id="LC67" class="blob-code blob-code-inner js-file-line"> Tryp_T.transcriptomicProcess(arguments,argdict)</td>
|
|
|
991 </tr>
|
|
|
992 <tr>
|
|
|
993 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
|
|
|
994 <td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_assemble<span class="pl-pds">'</span></span>:</td>
|
|
|
995 </tr>
|
|
|
996 <tr>
|
|
|
997 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
|
|
|
998 <td id="LC69" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>kmers<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>,<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>:<span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>:<span class="pl-c1">8</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">9</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">10</span>}</td>
|
|
|
999 </tr>
|
|
|
1000 <tr>
|
|
|
1001 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
|
|
|
1002 <td id="LC70" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_assemble(arguments,argdict)</td>
|
|
|
1003 </tr>
|
|
|
1004 <tr>
|
|
|
1005 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
|
|
|
1006 <td id="LC71" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_contigs<span class="pl-pds">'</span></span>:</td>
|
|
|
1007 </tr>
|
|
|
1008 <tr>
|
|
|
1009 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
|
|
|
1010 <td id="LC72" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>}</td>
|
|
|
1011 </tr>
|
|
|
1012 <tr>
|
|
|
1013 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
|
|
|
1014 <td id="LC73" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_contigs(arguments,argdict)</td>
|
|
|
1015 </tr>
|
|
|
1016 <tr>
|
|
|
1017 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
|
|
|
1018 <td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_transcript<span class="pl-pds">'</span></span>:</td>
|
|
|
1019 </tr>
|
|
|
1020 <tr>
|
|
|
1021 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
|
|
|
1022 <td id="LC75" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>: <span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>: <span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>: <span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>: <span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>: <span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>: <span class="pl-c1">8</span>}</td>
|
|
|
1023 </tr>
|
|
|
1024 <tr>
|
|
|
1025 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
|
|
|
1026 <td id="LC76" class="blob-code blob-code-inner js-file-line"> Tryp_V_T.transcriptomicProcess(arguments,argdict)</td>
|
|
|
1027 </tr>
|
|
|
1028 <tr>
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1029 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
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1030 <td id="LC77" class="blob-code blob-code-inner js-file-line">
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1031 </td>
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1032 </tr>
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1033 <tr>
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1034 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
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1035 <td id="LC78" class="blob-code blob-code-inner js-file-line">
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1036 </td>
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1037 </tr>
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1038 <tr>
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1039 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
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1040 <td id="LC79" class="blob-code blob-code-inner js-file-line">sys.exit()</td>
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1041 </tr>
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1042 <tr>
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1043 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
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1044 <td id="LC80" class="blob-code blob-code-inner js-file-line">
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1045 </td>
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1046 </tr>
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1047 </table>
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1048
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1049 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
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1050 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar">
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1051 <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg>
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1052 </summary>
|
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|
1053 <details-menu>
|
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1054 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
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1055 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li>
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1056 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li>
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1057 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/johnheap/VAPPER-Galaxy/blame/a4e16d71fe985f389930c02f94354b87d3aabadb/Vap.py">View git blame</a></li>
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1058 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li>
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1059 </ul>
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1060 </details-menu>
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1061 </details>
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1062
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1063 </div>
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1064
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1065 </div>
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1066
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1067
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1068
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1069 <details class="details-reset details-overlay details-overlay-dark">
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1070 <summary data-hotkey="l" aria-label="Jump to line"></summary>
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1071 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
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1072 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" />
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1073 <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus>
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1074 <button type="submit" class="btn" data-close-dialog>Go</button>
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1075 </form> </details-dialog>
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1076 </details>
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1077
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1078
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1079
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1080 </div>
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1081 <div class="modal-backdrop js-touch-events"></div>
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1082 </div>
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1083
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1084 </main>
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1085 </div>
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1086
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1087
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1088 </div>
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1089
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1090
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1091 <div class="footer container-lg width-full p-responsive" role="contentinfo">
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1092 <div class="position-relative d-flex flex-row-reverse flex-lg-row flex-wrap flex-lg-nowrap flex-justify-center flex-lg-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light ">
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1093 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
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1094 <li class="mr-3 mr-lg-0">© 2019 <span title="0.25049s from unicorn-7f8445f78c-hj7b2">GitHub</span>, Inc.</li>
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1099 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
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1100 </ul>
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1101
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1102 <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com">
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1103 <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
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1104 </a>
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1105 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
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1106 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li>
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1111 <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>
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1112
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1113 </ul>
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1114 </div>
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1115 <div class="d-flex flex-justify-center pb-6">
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1116 <span class="f6 text-gray-light"></span>
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1117 </div>
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1118 </div>
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1119
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1120
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1121
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1122 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
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1123 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
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1124 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
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1125 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
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1126 </button>
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1127 You can’t perform that action at this time.
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1128 </div>
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1129
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1130
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|
1131 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
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1132 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
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1133
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1134 <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script>
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1135
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1136
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1137
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|
1138 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
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1139 >
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|
1140 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
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1141 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
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1142 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
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1143 </div>
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1144 <template id="site-details-dialog">
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1145 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
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1146 <summary role="button" aria-label="Close dialog"></summary>
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1147 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
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1148 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
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1149 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
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1150 </button>
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1151 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
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1152 </details-dialog>
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1153 </details>
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1154 </template>
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1155
|
|
|
1156 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
|
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1157 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
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1158 </div>
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1159 </div>
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1160
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1161 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
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1162
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1163 </body>
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1164 </html>
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1165
|
