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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=OeWfhCkNlueqmf+vlMZUOIoZL/xaxMnWSzEKmM+a3P/55zFIrfSMdNtX4Lcjm/pZKDqzddz2DGdPMz+4X5/nxg=="
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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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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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|
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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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|
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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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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">* Galaxy Version</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"></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"> * Copyright 2019 University of Liverpool</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"> * Author John Heap, Computational Biology Facility, UoL</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"> * Based on original scripts of Sara Silva Silva Pereira, Institute of Infection and Global Health, UoL</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"> *</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"> * Licensed under the Apache License, Version 2.0 (the "License");</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"> * you may not use this file except in compliance with the License.</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"> * You may obtain a copy of the License at</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"> * http://www.apache.org/licenses/LICENSE-2.0</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"> *</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"> * Unless required by applicable law or agreed to in writing, software</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"> * distributed under the License is distributed on an "AS IS" BASIS,</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"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</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"> * See the License for the specific language governing permissions and</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"> * limitations under the License.</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-s"> *</span></td>
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794 </tr>
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802 </td>
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803 </tr>
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807 </td>
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808 </tr>
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811 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td>
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812 </tr>
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813 <tr>
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814 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
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815 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td>
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816 </tr>
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817 <tr>
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818 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
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819 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td>
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820 </tr>
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821 <tr>
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822 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
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823 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td>
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824 </tr>
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825 <tr>
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826 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
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827 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
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828 </tr>
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829 <tr>
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830 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
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831 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td>
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832 </tr>
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834 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
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835 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> import matplotlib as mpl</span></td>
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836 </tr>
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837 <tr>
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838 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
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839 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> mpl.use('Agg')</span></td>
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840 </tr>
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841 <tr>
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842 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
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843 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td>
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844 </tr>
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845 <tr>
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846 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
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847 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> numpy <span class="pl-k">as</span> np</td>
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848 </tr>
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849 <tr>
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852 </td>
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853 </tr>
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854 <tr>
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855 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
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856 <td id="LC34" class="blob-code blob-code-inner js-file-line">
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857 </td>
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858 </tr>
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859 <tr>
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860 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
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861 <td id="LC35" class="blob-code blob-code-inner js-file-line">
|
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862 </td>
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863 </tr>
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864 <tr>
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|
865 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
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866 <td id="LC36" class="blob-code blob-code-inner js-file-line">
|
|
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867 </td>
|
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868 </tr>
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869 <tr>
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870 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
|
|
|
871 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> copies the user provided Fasta file to data/reference/file/file.fasta</span></td>
|
|
|
872 </tr>
|
|
|
873 <tr>
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|
874 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
|
|
|
875 <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">uploadUserReferenceFastq</span>(<span class="pl-smi">refFastq</span>):</td>
|
|
|
876 </tr>
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877 <tr>
|
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|
878 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
|
|
|
879 <td id="LC39" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td>
|
|
|
880 </tr>
|
|
|
881 <tr>
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|
|
882 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
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|
|
883 <td id="LC40" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> 'mydata/test.fasta' -> 'test'</span></td>
|
|
|
884 </tr>
|
|
|
885 <tr>
|
|
|
886 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
|
|
|
887 <td id="LC41" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td>
|
|
|
888 </tr>
|
|
|
889 <tr>
|
|
|
890 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
|
|
|
891 <td id="LC42" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-c"><span class="pl-c">#</span>propose putting file in '/data/reference/ref/</span></td>
|
|
|
892 </tr>
|
|
|
893 <tr>
|
|
|
894 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
|
|
|
895 <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-k">not</span> os.path.isdir(refDir): <span class="pl-c"><span class="pl-c">#</span> if directory data/Reference/ref doesn't exist</span></td>
|
|
|
896 </tr>
|
|
|
897 <tr>
|
|
|
898 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
|
|
|
899 <td id="LC44" class="blob-code blob-code-inner js-file-line"> os.mkdir(refDir)</td>
|
|
|
900 </tr>
|
|
|
901 <tr>
|
|
|
902 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
|
|
|
903 <td id="LC45" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> refDir<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span></td>
|
|
|
904 </tr>
|
|
|
905 <tr>
|
|
|
906 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
|
|
|
907 <td id="LC46" class="blob-code blob-code-inner js-file-line"> shutil.copy(refFastq, refPath <span class="pl-k">+</span> refBase) <span class="pl-c"><span class="pl-c">#</span>copy reference file into the directory</span></td>
|
|
|
908 </tr>
|
|
|
909 <tr>
|
|
|
910 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
|
|
|
911 <td id="LC47" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2-build <span class="pl-pds">"</span></span> <span class="pl-k">+</span> refPath <span class="pl-k">+</span> refBase<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span><span class="pl-k">+</span>refPath<span class="pl-k">+</span>ref</td>
|
|
|
912 </tr>
|
|
|
913 <tr>
|
|
|
914 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
|
|
|
915 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>Building the bowtie2 reference files.<span class="pl-pds">"</span></span>)</td>
|
|
|
916 </tr>
|
|
|
917 <tr>
|
|
|
918 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
|
|
|
919 <td id="LC49" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
920 </tr>
|
|
|
921 <tr>
|
|
|
922 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
|
|
|
923 <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td>
|
|
|
924 </tr>
|
|
|
925 <tr>
|
|
|
926 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
|
|
|
927 <td id="LC51" class="blob-code blob-code-inner js-file-line">
|
|
|
928 </td>
|
|
|
929 </tr>
|
|
|
930 <tr>
|
|
|
931 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
|
|
|
932 <td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptMapping</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">refFastq</span>, <span class="pl-smi">forwardFN</span>, <span class="pl-smi">reverseFN</span>):</td>
|
|
|
933 </tr>
|
|
|
934 <tr>
|
|
|
935 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
|
|
|
936 <td id="LC53" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> where is our Reference data?</span></td>
|
|
|
937 </tr>
|
|
|
938 <tr>
|
|
|
939 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
|
|
|
940 <td id="LC54" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td>
|
|
|
941 </tr>
|
|
|
942 <tr>
|
|
|
943 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
|
|
|
944 <td id="LC55" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>]</td>
|
|
|
945 </tr>
|
|
|
946 <tr>
|
|
|
947 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
|
|
|
948 <td id="LC56" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
|
|
|
949 </tr>
|
|
|
950 <tr>
|
|
|
951 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
|
|
|
952 <td id="LC57" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span></td>
|
|
|
953 </tr>
|
|
|
954 <tr>
|
|
|
955 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
|
|
|
956 <td id="LC58" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> refDir <span class="pl-k">+</span> ref</td>
|
|
|
957 </tr>
|
|
|
958 <tr>
|
|
|
959 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
|
|
|
960 <td id="LC59" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> now have reference file so we can proceed with the transcript mapping via bowtie2</span></td>
|
|
|
961 </tr>
|
|
|
962 <tr>
|
|
|
963 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
|
|
|
964 <td id="LC60" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2 -x <span class="pl-pds">"</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -1 <span class="pl-pds">"</span></span><span class="pl-k">+</span>forwardFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -2 <span class="pl-pds">"</span></span><span class="pl-k">+</span>reverseFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -S <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam<span class="pl-pds">"</span></span></td>
|
|
|
965 </tr>
|
|
|
966 <tr>
|
|
|
967 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
|
|
|
968 <td id="LC61" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
|
|
|
969 </tr>
|
|
|
970 <tr>
|
|
|
971 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
|
|
|
972 <td id="LC62" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>) <span class="pl-c"><span class="pl-c">#</span>outputs a name.sam file</span></td>
|
|
|
973 </tr>
|
|
|
974 <tr>
|
|
|
975 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
|
|
|
976 <td id="LC63" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td>
|
|
|
977 </tr>
|
|
|
978 <tr>
|
|
|
979 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
|
|
|
980 <td id="LC64" class="blob-code blob-code-inner js-file-line">
|
|
|
981 </td>
|
|
|
982 </tr>
|
|
|
983 <tr>
|
|
|
984 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
|
|
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985 <td id="LC65" class="blob-code blob-code-inner js-file-line">
|
|
|
986 </td>
|
|
|
987 </tr>
|
|
|
988 <tr>
|
|
|
989 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
|
|
|
990 <td id="LC66" class="blob-code blob-code-inner js-file-line">
|
|
|
991 </td>
|
|
|
992 </tr>
|
|
|
993 <tr>
|
|
|
994 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
|
|
|
995 <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">processSamFiles</span>(<span class="pl-smi">inputname</span>):</td>
|
|
|
996 </tr>
|
|
|
997 <tr>
|
|
|
998 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
|
|
|
999 <td id="LC68" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td>
|
|
|
1000 </tr>
|
|
|
1001 <tr>
|
|
|
1002 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
|
|
|
1003 <td id="LC69" class="blob-code blob-code-inner js-file-line"> samName <span class="pl-k">=</span> cur_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname</td>
|
|
|
1004 </tr>
|
|
|
1005 <tr>
|
|
|
1006 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
|
|
|
1007 <td id="LC70" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools view -bS <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam > <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span></td>
|
|
|
1008 </tr>
|
|
|
1009 <tr>
|
|
|
1010 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
|
|
|
1011 <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
|
|
|
1012 </tr>
|
|
|
1013 <tr>
|
|
|
1014 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
|
|
|
1015 <td id="LC72" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1016 </tr>
|
|
|
1017 <tr>
|
|
|
1018 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
|
|
|
1019 <td id="LC73" class="blob-code blob-code-inner js-file-line">
|
|
|
1020 </td>
|
|
|
1021 </tr>
|
|
|
1022 <tr>
|
|
|
1023 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
|
|
|
1024 <td id="LC74" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools sort <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span></td>
|
|
|
1025 </tr>
|
|
|
1026 <tr>
|
|
|
1027 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
|
|
|
1028 <td id="LC75" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>argstring = <span class="pl-pds">"</span></span><span class="pl-k">+</span>argString)</td>
|
|
|
1029 </tr>
|
|
|
1030 <tr>
|
|
|
1031 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
|
|
|
1032 <td id="LC76" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1033 </tr>
|
|
|
1034 <tr>
|
|
|
1035 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
|
|
|
1036 <td id="LC77" class="blob-code blob-code-inner js-file-line">
|
|
|
1037 </td>
|
|
|
1038 </tr>
|
|
|
1039 <tr>
|
|
|
1040 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
|
|
|
1041 <td id="LC78" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools index <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span></td>
|
|
|
1042 </tr>
|
|
|
1043 <tr>
|
|
|
1044 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
|
|
|
1045 <td id="LC79" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>argstring = <span class="pl-pds">"</span></span> <span class="pl-k">+</span> argString)</td>
|
|
|
1046 </tr>
|
|
|
1047 <tr>
|
|
|
1048 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
|
|
|
1049 <td id="LC80" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1050 </tr>
|
|
|
1051 <tr>
|
|
|
1052 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
|
|
|
1053 <td id="LC81" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c"><span class="pl-c">#</span>we have saved out the relevent name.bam, name.sorted and name.sorted.bai files</span></td>
|
|
|
1054 </tr>
|
|
|
1055 <tr>
|
|
|
1056 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
|
|
|
1057 <td id="LC82" class="blob-code blob-code-inner js-file-line">
|
|
|
1058 </td>
|
|
|
1059 </tr>
|
|
|
1060 <tr>
|
|
|
1061 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
|
|
|
1062 <td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> we will not have the .gtf file so call cufflinks without -G option</span></td>
|
|
|
1063 </tr>
|
|
|
1064 <tr>
|
|
|
1065 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
|
|
|
1066 <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptAbundance</span>(<span class="pl-smi">inputname</span>):</td>
|
|
|
1067 </tr>
|
|
|
1068 <tr>
|
|
|
1069 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
|
|
|
1070 <td id="LC85" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>cufflinks -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.cuff -u -p 8 <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span></td>
|
|
|
1071 </tr>
|
|
|
1072 <tr>
|
|
|
1073 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
|
|
|
1074 <td id="LC86" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td>
|
|
|
1075 </tr>
|
|
|
1076 <tr>
|
|
|
1077 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
|
|
|
1078 <td id="LC87" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span>remove name.sorted</span></td>
|
|
|
1079 </tr>
|
|
|
1080 <tr>
|
|
|
1081 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
|
|
|
1082 <td id="LC88" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span>)</td>
|
|
|
1083 </tr>
|
|
|
1084 <tr>
|
|
|
1085 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
|
|
|
1086 <td id="LC89" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span>)</td>
|
|
|
1087 </tr>
|
|
|
1088 <tr>
|
|
|
1089 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
|
|
|
1090 <td id="LC90" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td>
|
|
|
1091 </tr>
|
|
|
1092 <tr>
|
|
|
1093 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
|
|
|
1094 <td id="LC91" class="blob-code blob-code-inner js-file-line">
|
|
|
1095 </td>
|
|
|
1096 </tr>
|
|
|
1097 <tr>
|
|
|
1098 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
|
|
|
1099 <td id="LC92" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptsForBlast</span>(<span class="pl-smi">name</span>, <span class="pl-smi">refFastq</span>):</td>
|
|
|
1100 </tr>
|
|
|
1101 <tr>
|
|
|
1102 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
|
|
|
1103 <td id="LC93" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> quick and dirty just to see.</span></td>
|
|
|
1104 </tr>
|
|
|
1105 <tr>
|
|
|
1106 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
|
|
|
1107 <td id="LC94" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td>
|
|
|
1108 </tr>
|
|
|
1109 <tr>
|
|
|
1110 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
|
|
|
1111 <td id="LC95" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> 'mydata/test.fasta' -> 'test'</span></td>
|
|
|
1112 </tr>
|
|
|
1113 <tr>
|
|
|
1114 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
|
|
|
1115 <td id="LC96" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td>
|
|
|
1116 </tr>
|
|
|
1117 <tr>
|
|
|
1118 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
|
|
|
1119 <td id="LC97" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> refBase <span class="pl-c"><span class="pl-c">#</span> eg refPath = data/Reference/Trinity/Trinity.fasta</span></td>
|
|
|
1120 </tr>
|
|
|
1121 <tr>
|
|
|
1122 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
|
|
|
1123 <td id="LC98" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> used for dirty # refPath = 'Trinity.fasta' # dirty one</span></td>
|
|
|
1124 </tr>
|
|
|
1125 <tr>
|
|
|
1126 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
|
|
|
1127 <td id="LC99" class="blob-code blob-code-inner js-file-line"> track_df <span class="pl-k">=</span> pd.read_csv(name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>.cuff/genes.fpkm_tracking<span class="pl-pds">'</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>)</td>
|
|
|
1128 </tr>
|
|
|
1129 <tr>
|
|
|
1130 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
|
|
|
1131 <td id="LC100" class="blob-code blob-code-inner js-file-line"> names <span class="pl-k">=</span> track_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>]</td>
|
|
|
1132 </tr>
|
|
|
1133 <tr>
|
|
|
1134 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
|
|
|
1135 <td id="LC101" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(len(names))</span></td>
|
|
|
1136 </tr>
|
|
|
1137 <tr>
|
|
|
1138 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
|
|
|
1139 <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(names[:5])</span></td>
|
|
|
1140 </tr>
|
|
|
1141 <tr>
|
|
|
1142 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
|
|
|
1143 <td id="LC103" class="blob-code blob-code-inner js-file-line">
|
|
|
1144 </td>
|
|
|
1145 </tr>
|
|
|
1146 <tr>
|
|
|
1147 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
|
|
|
1148 <td id="LC104" class="blob-code blob-code-inner js-file-line"> nlist <span class="pl-k">=</span> []</td>
|
|
|
1149 </tr>
|
|
|
1150 <tr>
|
|
|
1151 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
|
|
|
1152 <td id="LC105" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(names)):</td>
|
|
|
1153 </tr>
|
|
|
1154 <tr>
|
|
|
1155 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
|
|
|
1156 <td id="LC106" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> names[n].find(<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>)</td>
|
|
|
1157 </tr>
|
|
|
1158 <tr>
|
|
|
1159 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
|
|
|
1160 <td id="LC107" class="blob-code blob-code-inner js-file-line"> nlist.append(names[n][:i])</td>
|
|
|
1161 </tr>
|
|
|
1162 <tr>
|
|
|
1163 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
|
|
|
1164 <td id="LC108" class="blob-code blob-code-inner js-file-line"> nameset <span class="pl-k">=</span> <span class="pl-c1">set</span>(nlist) <span class="pl-c"><span class="pl-c">#</span>get unique.</span></td>
|
|
|
1165 </tr>
|
|
|
1166 <tr>
|
|
|
1167 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
|
|
|
1168 <td id="LC109" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(refPath, <span class="pl-s"><span class="pl-pds">'</span>r<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> myRef:</td>
|
|
|
1169 </tr>
|
|
|
1170 <tr>
|
|
|
1171 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
|
|
|
1172 <td id="LC110" class="blob-code blob-code-inner js-file-line"> refData <span class="pl-k">=</span> myRef.read()</td>
|
|
|
1173 </tr>
|
|
|
1174 <tr>
|
|
|
1175 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
|
|
|
1176 <td id="LC111" class="blob-code blob-code-inner js-file-line"> refData<span class="pl-k">=</span> refData<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n</span>><span class="pl-pds">'</span></span></td>
|
|
|
1177 </tr>
|
|
|
1178 <tr>
|
|
|
1179 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
|
|
|
1180 <td id="LC112" class="blob-code blob-code-inner js-file-line">
|
|
|
1181 </td>
|
|
|
1182 </tr>
|
|
|
1183 <tr>
|
|
|
1184 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
|
|
|
1185 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">'</span>_for_blast.fa<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> outfile:</td>
|
|
|
1186 </tr>
|
|
|
1187 <tr>
|
|
|
1188 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
|
|
|
1189 <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> trans_id <span class="pl-k">in</span> nameset:</td>
|
|
|
1190 </tr>
|
|
|
1191 <tr>
|
|
|
1192 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
|
|
|
1193 <td id="LC115" class="blob-code blob-code-inner js-file-line"> namepos <span class="pl-k">=</span> refData.find(trans_id)</td>
|
|
|
1194 </tr>
|
|
|
1195 <tr>
|
|
|
1196 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
|
|
|
1197 <td id="LC116" class="blob-code blob-code-inner js-file-line"> endpos <span class="pl-k">=</span> refData.find(<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>, namepos)</td>
|
|
|
1198 </tr>
|
|
|
1199 <tr>
|
|
|
1200 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
|
|
|
1201 <td id="LC117" class="blob-code blob-code-inner js-file-line"> outfile.write(<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span><span class="pl-k">+</span>refData[namepos:endpos])</td>
|
|
|
1202 </tr>
|
|
|
1203 <tr>
|
|
|
1204 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
|
|
|
1205 <td id="LC118" class="blob-code blob-code-inner js-file-line">
|
|
|
1206 </td>
|
|
|
1207 </tr>
|
|
|
1208 <tr>
|
|
|
1209 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
|
|
|
1210 <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td>
|
|
|
1211 </tr>
|
|
|
1212 <tr>
|
|
|
1213 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
|
|
|
1214 <td id="LC120" class="blob-code blob-code-inner js-file-line">
|
|
|
1215 </td>
|
|
|
1216 </tr>
|
|
|
1217 <tr>
|
|
|
1218 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
|
|
|
1219 <td id="LC121" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">html_resource</span>, <span class="pl-smi">database</span>):</td>
|
|
|
1220 </tr>
|
|
|
1221 <tr>
|
|
|
1222 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
|
|
|
1223 <td id="LC122" class="blob-code blob-code-inner js-file-line"> db_path <span class="pl-k">=</span> database</td>
|
|
|
1224 </tr>
|
|
|
1225 <tr>
|
|
|
1226 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
|
|
|
1227 <td id="LC123" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>blastx -db <span class="pl-pds">"</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -query <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_for_blast.fa -outfmt 10 -out <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span></td>
|
|
|
1228 </tr>
|
|
|
1229 <tr>
|
|
|
1230 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
|
|
|
1231 <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
|
|
|
1232 </tr>
|
|
|
1233 <tr>
|
|
|
1234 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
|
|
|
1235 <td id="LC125" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1236 </tr>
|
|
|
1237 <tr>
|
|
|
1238 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
|
|
|
1239 <td id="LC126" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
|
|
|
1240 </tr>
|
|
|
1241 <tr>
|
|
|
1242 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
|
|
|
1243 <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in blastall<span class="pl-pds">"</span></span></td>
|
|
|
1244 </tr>
|
|
|
1245 <tr>
|
|
|
1246 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
|
|
|
1247 <td id="LC128" class="blob-code blob-code-inner js-file-line"> blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span>)</td>
|
|
|
1248 </tr>
|
|
|
1249 <tr>
|
|
|
1250 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
|
|
|
1251 <td id="LC129" class="blob-code blob-code-inner js-file-line"> blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>mismatch<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>gapopen<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qend<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>sstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>send<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]</td>
|
|
|
1252 </tr>
|
|
|
1253 <tr>
|
|
|
1254 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
|
|
|
1255 <td id="LC130" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]<span class="pl-k">>=</span><span class="pl-c1">70</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">100</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>] <span class="pl-k"><=</span><span class="pl-c1">0.001</span>) ]</td>
|
|
|
1256 </tr>
|
|
|
1257 <tr>
|
|
|
1258 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
|
|
|
1259 <td id="LC131" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]] <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td>
|
|
|
1260 </tr>
|
|
|
1261 <tr>
|
|
|
1262 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
|
|
|
1263 <td id="LC132" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> need to allocate the transcripts (if allocated more than once to the phylotype with least error.</span></td>
|
|
|
1264 </tr>
|
|
|
1265 <tr>
|
|
|
1266 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
|
|
|
1267 <td id="LC133" class="blob-code blob-code-inner js-file-line"> transcripts <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>]</td>
|
|
|
1268 </tr>
|
|
|
1269 <tr>
|
|
|
1270 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
|
|
|
1271 <td id="LC134" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>])</td>
|
|
|
1272 </tr>
|
|
|
1273 <tr>
|
|
|
1274 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
|
|
|
1275 <td id="LC135" class="blob-code blob-code-inner js-file-line"> transSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(transcripts)</td>
|
|
|
1276 </tr>
|
|
|
1277 <tr>
|
|
|
1278 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
|
|
|
1279 <td id="LC136" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> t <span class="pl-k">in</span> transSet:</td>
|
|
|
1280 </tr>
|
|
|
1281 <tr>
|
|
|
1282 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
|
|
|
1283 <td id="LC137" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> blastResult_df[(blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> t)]</td>
|
|
|
1284 </tr>
|
|
|
1285 <tr>
|
|
|
1286 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
|
|
|
1287 <td id="LC138" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get one with smallest error value</span></td>
|
|
|
1288 </tr>
|
|
|
1289 <tr>
|
|
|
1290 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
|
|
|
1291 <td id="LC139" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(t + ":")</span></td>
|
|
|
1292 </tr>
|
|
|
1293 <tr>
|
|
|
1294 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
|
|
|
1295 <td id="LC140" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(temp_df)</span></td>
|
|
|
1296 </tr>
|
|
|
1297 <tr>
|
|
|
1298 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
|
|
|
1299 <td id="LC141" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> temp_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>])</td>
|
|
|
1300 </tr>
|
|
|
1301 <tr>
|
|
|
1302 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
|
|
|
1303 <td id="LC142" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> b_df.append(temp_df.iloc[[<span class="pl-c1">0</span>]])</td>
|
|
|
1304 </tr>
|
|
|
1305 <tr>
|
|
|
1306 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
|
|
|
1307 <td id="LC143" class="blob-code blob-code-inner js-file-line">
|
|
|
1308 </td>
|
|
|
1309 </tr>
|
|
|
1310 <tr>
|
|
|
1311 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
|
|
|
1312 <td id="LC144" class="blob-code blob-code-inner js-file-line"> b_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>])</td>
|
|
|
1313 </tr>
|
|
|
1314 <tr>
|
|
|
1315 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
|
|
|
1316 <td id="LC145" class="blob-code blob-code-inner js-file-line"> b_df.to_csv(test_name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">'</span>_transcript.csv<span class="pl-pds">'</span></span>)</td>
|
|
|
1317 </tr>
|
|
|
1318 <tr>
|
|
|
1319 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
|
|
|
1320 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> b_df</td>
|
|
|
1321 </tr>
|
|
|
1322 <tr>
|
|
|
1323 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
|
|
|
1324 <td id="LC147" class="blob-code blob-code-inner js-file-line">
|
|
|
1325 </td>
|
|
|
1326 </tr>
|
|
|
1327 <tr>
|
|
|
1328 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
|
|
|
1329 <td id="LC148" class="blob-code blob-code-inner js-file-line">
|
|
|
1330 </td>
|
|
|
1331 </tr>
|
|
|
1332 <tr>
|
|
|
1333 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
|
|
|
1334 <td id="LC149" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createMultiHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">composite_df</span>):</td>
|
|
|
1335 </tr>
|
|
|
1336 <tr>
|
|
|
1337 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
|
|
|
1338 <td id="LC150" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td>
|
|
|
1339 </tr>
|
|
|
1340 <tr>
|
|
|
1341 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
|
|
|
1342 <td id="LC151" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span></title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td>
|
|
|
1343 </tr>
|
|
|
1344 <tr>
|
|
|
1345 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
|
|
|
1346 <td id="LC152" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Sample name: <span class="pl-pds">"</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]</td>
|
|
|
1347 </tr>
|
|
|
1348 <tr>
|
|
|
1349 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
|
|
|
1350 <td id="LC153" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td>
|
|
|
1351 </tr>
|
|
|
1352 <tr>
|
|
|
1353 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
|
|
|
1354 <td id="LC154" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Legend: <span class="pl-pds">"</span></span> \</td>
|
|
|
1355 </tr>
|
|
|
1356 <tr>
|
|
|
1357 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
|
|
|
1358 <td id="LC155" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptomes. <span class="pl-pds">"</span></span> \</td>
|
|
|
1359 </tr>
|
|
|
1360 <tr>
|
|
|
1361 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
|
|
|
1362 <td id="LC156" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">"</span></span> \</td>
|
|
|
1363 </tr>
|
|
|
1364 <tr>
|
|
|
1365 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
|
|
|
1366 <td id="LC157" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">"</span></span> \</td>
|
|
|
1367 </tr>
|
|
|
1368 <tr>
|
|
|
1369 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
|
|
|
1370 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">"</span></span> \</td>
|
|
|
1371 </tr>
|
|
|
1372 <tr>
|
|
|
1373 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
|
|
|
1374 <td id="LC159" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>(Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td>
|
|
|
1375 </tr>
|
|
|
1376 <tr>
|
|
|
1377 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
|
|
|
1378 <td id="LC160" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td>
|
|
|
1379 </tr>
|
|
|
1380 <tr>
|
|
|
1381 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
|
|
|
1382 <td id="LC161" class="blob-code blob-code-inner js-file-line">
|
|
|
1383 </td>
|
|
|
1384 </tr>
|
|
|
1385 <tr>
|
|
|
1386 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
|
|
|
1387 <td id="LC162" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><span class="pl-pds">"</span></span></td>
|
|
|
1388 </tr>
|
|
|
1389 <tr>
|
|
|
1390 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
|
|
|
1391 <td id="LC163" class="blob-code blob-code-inner js-file-line"> wLists <span class="pl-k">=</span> []</td>
|
|
|
1392 </tr>
|
|
|
1393 <tr>
|
|
|
1394 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
|
|
|
1395 <td id="LC164" class="blob-code blob-code-inner js-file-line">
|
|
|
1396 </td>
|
|
|
1397 </tr>
|
|
|
1398 <tr>
|
|
|
1399 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
|
|
|
1400 <td id="LC165" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>,<span class="pl-c1">len</span>(labelList)):</td>
|
|
|
1401 </tr>
|
|
|
1402 <tr>
|
|
|
1403 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
|
|
|
1404 <td id="LC166" class="blob-code blob-code-inner js-file-line"> wLists.append(composite_df[labelList[j]])</td>
|
|
|
1405 </tr>
|
|
|
1406 <tr>
|
|
|
1407 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
|
|
|
1408 <td id="LC167" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><th><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(labelList[j]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></th><span class="pl-pds">"</span></span></td>
|
|
|
1409 </tr>
|
|
|
1410 <tr>
|
|
|
1411 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
|
|
|
1412 <td id="LC168" class="blob-code blob-code-inner js-file-line">
|
|
|
1413 </td>
|
|
|
1414 </tr>
|
|
|
1415 <tr>
|
|
|
1416 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
|
|
|
1417 <td id="LC169" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">+</span> header</td>
|
|
|
1418 </tr>
|
|
|
1419 <tr>
|
|
|
1420 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
|
|
|
1421 <td id="LC170" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td>
|
|
|
1422 </tr>
|
|
|
1423 <tr>
|
|
|
1424 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
|
|
|
1425 <td id="LC171" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> composite_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td>
|
|
|
1426 </tr>
|
|
|
1427 <tr>
|
|
|
1428 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
|
|
|
1429 <td id="LC172" class="blob-code blob-code-inner js-file-line">
|
|
|
1430 </td>
|
|
|
1431 </tr>
|
|
|
1432 <tr>
|
|
|
1433 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
|
|
|
1434 <td id="LC173" class="blob-code blob-code-inner js-file-line">
|
|
|
1435 </td>
|
|
|
1436 </tr>
|
|
|
1437 <tr>
|
|
|
1438 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
|
|
|
1439 <td id="LC174" class="blob-code blob-code-inner js-file-line">
|
|
|
1440 </td>
|
|
|
1441 </tr>
|
|
|
1442 <tr>
|
|
|
1443 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
|
|
|
1444 <td id="LC175" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(composite_df)):</td>
|
|
|
1445 </tr>
|
|
|
1446 <tr>
|
|
|
1447 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
|
|
|
1448 <td id="LC176" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phyList[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><span class="pl-pds">"</span></span></td>
|
|
|
1449 </tr>
|
|
|
1450 <tr>
|
|
|
1451 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
|
|
|
1452 <td id="LC177" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span>):</td>
|
|
|
1453 </tr>
|
|
|
1454 <tr>
|
|
|
1455 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
|
|
|
1456 <td id="LC178" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(j)</span></td>
|
|
|
1457 </tr>
|
|
|
1458 <tr>
|
|
|
1459 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
|
|
|
1460 <td id="LC179" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(wLists[j][i], <span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td>
|
|
|
1461 </tr>
|
|
|
1462 <tr>
|
|
|
1463 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
|
|
|
1464 <td id="LC180" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><span class="pl-pds">"</span></span></td>
|
|
|
1465 </tr>
|
|
|
1466 <tr>
|
|
|
1467 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
|
|
|
1468 <td id="LC181" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-cce">\n</span><span class="pl-pds">"</span></span></td>
|
|
|
1469 </tr>
|
|
|
1470 <tr>
|
|
|
1471 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
|
|
|
1472 <td id="LC182" class="blob-code blob-code-inner js-file-line">
|
|
|
1473 </td>
|
|
|
1474 </tr>
|
|
|
1475 <tr>
|
|
|
1476 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
|
|
|
1477 <td id="LC183" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td>
|
|
|
1478 </tr>
|
|
|
1479 <tr>
|
|
|
1480 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
|
|
|
1481 <td id="LC184" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span></h3><span class="pl-pds">"</span></span></td>
|
|
|
1482 </tr>
|
|
|
1483 <tr>
|
|
|
1484 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
|
|
|
1485 <td id="LC185" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td>
|
|
|
1486 </tr>
|
|
|
1487 <tr>
|
|
|
1488 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
|
|
|
1489 <td id="LC186" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
|
|
|
1490 </tr>
|
|
|
1491 <tr>
|
|
|
1492 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
|
|
|
1493 <td id="LC187" class="blob-code blob-code-inner js-file-line">
|
|
|
1494 </td>
|
|
|
1495 </tr>
|
|
|
1496 <tr>
|
|
|
1497 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
|
|
|
1498 <td id="LC188" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td>
|
|
|
1499 </tr>
|
|
|
1500 <tr>
|
|
|
1501 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
|
|
|
1502 <td id="LC189" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
|
|
|
1503 </tr>
|
|
|
1504 <tr>
|
|
|
1505 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
|
|
|
1506 <td id="LC190" class="blob-code blob-code-inner js-file-line">
|
|
|
1507 </td>
|
|
|
1508 </tr>
|
|
|
1509 <tr>
|
|
|
1510 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
|
|
|
1511 <td id="LC191" class="blob-code blob-code-inner js-file-line">
|
|
|
1512 </td>
|
|
|
1513 </tr>
|
|
|
1514 <tr>
|
|
|
1515 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
|
|
|
1516 <td id="LC192" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">sum_df</span>):</td>
|
|
|
1517 </tr>
|
|
|
1518 <tr>
|
|
|
1519 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
|
|
|
1520 <td id="LC193" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
|
|
|
1521 </tr>
|
|
|
1522 <tr>
|
|
|
1523 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
|
|
|
1524 <td id="LC194" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span></title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td>
|
|
|
1525 </tr>
|
|
|
1526 <tr>
|
|
|
1527 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
|
|
|
1528 <td id="LC195" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Sample name: <span class="pl-pds">"</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]</td>
|
|
|
1529 </tr>
|
|
|
1530 <tr>
|
|
|
1531 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
|
|
|
1532 <td id="LC196" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td>
|
|
|
1533 </tr>
|
|
|
1534 <tr>
|
|
|
1535 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
|
|
|
1536 <td id="LC197" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Legend: <span class="pl-pds">"</span></span> \</td>
|
|
|
1537 </tr>
|
|
|
1538 <tr>
|
|
|
1539 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
|
|
|
1540 <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptome. <span class="pl-pds">"</span></span> \</td>
|
|
|
1541 </tr>
|
|
|
1542 <tr>
|
|
|
1543 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
|
|
|
1544 <td id="LC199" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">"</span></span> \</td>
|
|
|
1545 </tr>
|
|
|
1546 <tr>
|
|
|
1547 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
|
|
|
1548 <td id="LC200" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">"</span></span> \</td>
|
|
|
1549 </tr>
|
|
|
1550 <tr>
|
|
|
1551 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
|
|
|
1552 <td id="LC201" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">"</span></span> \</td>
|
|
|
1553 </tr>
|
|
|
1554 <tr>
|
|
|
1555 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
|
|
|
1556 <td id="LC202" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>(Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td>
|
|
|
1557 </tr>
|
|
|
1558 <tr>
|
|
|
1559 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
|
|
|
1560 <td id="LC203" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td>
|
|
|
1561 </tr>
|
|
|
1562 <tr>
|
|
|
1563 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
|
|
|
1564 <td id="LC204" class="blob-code blob-code-inner js-file-line">
|
|
|
1565 </td>
|
|
|
1566 </tr>
|
|
|
1567 <tr>
|
|
|
1568 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
|
|
|
1569 <td id="LC205" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;table-layout: auto; margin-left:25%;text-align:center'><tr><th>Phylotype</th><span class="pl-pds">"</span></span> \</td>
|
|
|
1570 </tr>
|
|
|
1571 <tr>
|
|
|
1572 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
|
|
|
1573 <td id="LC206" class="blob-code blob-code-inner js-file-line"> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><th>Combined FPKM</th><th>Weighted Frequency</th></tr><span class="pl-pds">"</span></span></td>
|
|
|
1574 </tr>
|
|
|
1575 <tr>
|
|
|
1576 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
|
|
|
1577 <td id="LC207" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td>
|
|
|
1578 </tr>
|
|
|
1579 <tr>
|
|
|
1580 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
|
|
|
1581 <td id="LC208" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></td>
|
|
|
1582 </tr>
|
|
|
1583 <tr>
|
|
|
1584 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
|
|
|
1585 <td id="LC209" class="blob-code blob-code-inner js-file-line"> phySeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td>
|
|
|
1586 </tr>
|
|
|
1587 <tr>
|
|
|
1588 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
|
|
|
1589 <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> sacSeries = sum_df['saccver']</span></td>
|
|
|
1590 </tr>
|
|
|
1591 <tr>
|
|
|
1592 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
|
|
|
1593 <td id="LC211" class="blob-code blob-code-inner js-file-line"> fSeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>]</td>
|
|
|
1594 </tr>
|
|
|
1595 <tr>
|
|
|
1596 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
|
|
|
1597 <td id="LC212" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> fSeries.sum()</td>
|
|
|
1598 </tr>
|
|
|
1599 <tr>
|
|
|
1600 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
|
|
|
1601 <td id="LC213" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print("Total="+str(total))</span></td>
|
|
|
1602 </tr>
|
|
|
1603 <tr>
|
|
|
1604 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
|
|
|
1605 <td id="LC214" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum_df)):</td>
|
|
|
1606 </tr>
|
|
|
1607 <tr>
|
|
|
1608 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
|
|
|
1609 <td id="LC215" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(phySeries[i])</span></td>
|
|
|
1610 </tr>
|
|
|
1611 <tr>
|
|
|
1612 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
|
|
|
1613 <td id="LC216" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i], <span class="pl-s"><span class="pl-pds">'</span>.2f<span class="pl-pds">'</span></span>)</td>
|
|
|
1614 </tr>
|
|
|
1615 <tr>
|
|
|
1616 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
|
|
|
1617 <td id="LC217" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i]<span class="pl-k">/</span>total, <span class="pl-s"><span class="pl-pds">'</span>.2f<span class="pl-pds">'</span></span>)</td>
|
|
|
1618 </tr>
|
|
|
1619 <tr>
|
|
|
1620 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
|
|
|
1621 <td id="LC218" class="blob-code blob-code-inner js-file-line">
|
|
|
1622 </td>
|
|
|
1623 </tr>
|
|
|
1624 <tr>
|
|
|
1625 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
|
|
|
1626 <td id="LC219" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>w = format(weightList[i], '.4f')</span></td>
|
|
|
1627 </tr>
|
|
|
1628 <tr>
|
|
|
1629 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
|
|
|
1630 <td id="LC220" class="blob-code blob-code-inner js-file-line">
|
|
|
1631 </td>
|
|
|
1632 </tr>
|
|
|
1633 <tr>
|
|
|
1634 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
|
|
|
1635 <td id="LC221" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phySeries[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(w)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-pds">"</span></span></td>
|
|
|
1636 </tr>
|
|
|
1637 <tr>
|
|
|
1638 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
|
|
|
1639 <td id="LC222" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td>
|
|
|
1640 </tr>
|
|
|
1641 <tr>
|
|
|
1642 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
|
|
|
1643 <td id="LC223" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span></h3><span class="pl-pds">"</span></span></td>
|
|
|
1644 </tr>
|
|
|
1645 <tr>
|
|
|
1646 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
|
|
|
1647 <td id="LC224" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td>
|
|
|
1648 </tr>
|
|
|
1649 <tr>
|
|
|
1650 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
|
|
|
1651 <td id="LC225" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
|
|
|
1652 </tr>
|
|
|
1653 <tr>
|
|
|
1654 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
|
|
|
1655 <td id="LC226" class="blob-code blob-code-inner js-file-line">
|
|
|
1656 </td>
|
|
|
1657 </tr>
|
|
|
1658 <tr>
|
|
|
1659 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
|
|
|
1660 <td id="LC227" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td>
|
|
|
1661 </tr>
|
|
|
1662 <tr>
|
|
|
1663 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
|
|
|
1664 <td id="LC228" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
|
|
|
1665 </tr>
|
|
|
1666 <tr>
|
|
|
1667 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
|
|
|
1668 <td id="LC229" class="blob-code blob-code-inner js-file-line">
|
|
|
1669 </td>
|
|
|
1670 </tr>
|
|
|
1671 <tr>
|
|
|
1672 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
|
|
|
1673 <td id="LC230" class="blob-code blob-code-inner js-file-line">
|
|
|
1674 </td>
|
|
|
1675 </tr>
|
|
|
1676 <tr>
|
|
|
1677 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
|
|
|
1678 <td id="LC231" class="blob-code blob-code-inner js-file-line">
|
|
|
1679 </td>
|
|
|
1680 </tr>
|
|
|
1681 <tr>
|
|
|
1682 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
|
|
|
1683 <td id="LC232" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getPhyloNumber</span>(<span class="pl-smi">sac</span>):</td>
|
|
|
1684 </tr>
|
|
|
1685 <tr>
|
|
|
1686 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
|
|
|
1687 <td id="LC233" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> sac.find(<span class="pl-s"><span class="pl-pds">'</span>_<span class="pl-pds">'</span></span>)</td>
|
|
|
1688 </tr>
|
|
|
1689 <tr>
|
|
|
1690 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
|
|
|
1691 <td id="LC234" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c1">int</span>(sac[<span class="pl-c1">1</span>:i])</td>
|
|
|
1692 </tr>
|
|
|
1693 <tr>
|
|
|
1694 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
|
|
|
1695 <td id="LC235" class="blob-code blob-code-inner js-file-line">
|
|
|
1696 </td>
|
|
|
1697 </tr>
|
|
|
1698 <tr>
|
|
|
1699 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
|
|
|
1700 <td id="LC236" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">combineFPMK</span>(<span class="pl-smi">tdict</span>):</td>
|
|
|
1701 </tr>
|
|
|
1702 <tr>
|
|
|
1703 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
|
|
|
1704 <td id="LC237" class="blob-code blob-code-inner js-file-line"> fpkm_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>.cuff/genes.fpkm_tracking<span class="pl-pds">'</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>)</td>
|
|
|
1705 </tr>
|
|
|
1706 <tr>
|
|
|
1707 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
|
|
|
1708 <td id="LC238" class="blob-code blob-code-inner js-file-line">
|
|
|
1709 </td>
|
|
|
1710 </tr>
|
|
|
1711 <tr>
|
|
|
1712 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
|
|
|
1713 <td id="LC239" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t')</span></td>
|
|
|
1714 </tr>
|
|
|
1715 <tr>
|
|
|
1716 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
|
|
|
1717 <td id="LC240" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td>
|
|
|
1718 </tr>
|
|
|
1719 <tr>
|
|
|
1720 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
|
|
|
1721 <td id="LC241" class="blob-code blob-code-inner js-file-line"> fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>].apply(<span class="pl-k">lambda</span> <span class="pl-smi">names</span>: names[:names.find(<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>)])</td>
|
|
|
1722 </tr>
|
|
|
1723 <tr>
|
|
|
1724 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
|
|
|
1725 <td id="LC242" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td>
|
|
|
1726 </tr>
|
|
|
1727 <tr>
|
|
|
1728 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
|
|
|
1729 <td id="LC243" class="blob-code blob-code-inner js-file-line"> reducedBlast_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>_transcript.csv<span class="pl-pds">'</span></span>)</td>
|
|
|
1730 </tr>
|
|
|
1731 <tr>
|
|
|
1732 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
|
|
|
1733 <td id="LC244" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> reducedBlast_df = pd.read_csv('TrinityVT_transcript.csv')</span></td>
|
|
|
1734 </tr>
|
|
|
1735 <tr>
|
|
|
1736 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
|
|
|
1737 <td id="LC245" class="blob-code blob-code-inner js-file-line"> saccverSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(reducedBlast_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>])</td>
|
|
|
1738 </tr>
|
|
|
1739 <tr>
|
|
|
1740 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
|
|
|
1741 <td id="LC246" class="blob-code blob-code-inner js-file-line"> saccverList <span class="pl-k">=</span> <span class="pl-c1">list</span>(saccverSet)</td>
|
|
|
1742 </tr>
|
|
|
1743 <tr>
|
|
|
1744 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
|
|
|
1745 <td id="LC247" class="blob-code blob-code-inner js-file-line"> saccverList.sort()</td>
|
|
|
1746 </tr>
|
|
|
1747 <tr>
|
|
|
1748 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
|
|
|
1749 <td id="LC248" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(saccverList[:5])</span></td>
|
|
|
1750 </tr>
|
|
|
1751 <tr>
|
|
|
1752 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
|
|
|
1753 <td id="LC249" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>])</td>
|
|
|
1754 </tr>
|
|
|
1755 <tr>
|
|
|
1756 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
|
|
|
1757 <td id="LC250" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> sv <span class="pl-k">in</span> saccverList:</td>
|
|
|
1758 </tr>
|
|
|
1759 <tr>
|
|
|
1760 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
|
|
|
1761 <td id="LC251" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(sv)</span></td>
|
|
|
1762 </tr>
|
|
|
1763 <tr>
|
|
|
1764 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
|
|
|
1765 <td id="LC252" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> reducedBlast_df[reducedBlast_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> sv]</td>
|
|
|
1766 </tr>
|
|
|
1767 <tr>
|
|
|
1768 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
|
|
|
1769 <td id="LC253" class="blob-code blob-code-inner js-file-line"> qList <span class="pl-k">=</span> <span class="pl-c1">list</span>(temp_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>])</td>
|
|
|
1770 </tr>
|
|
|
1771 <tr>
|
|
|
1772 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
|
|
|
1773 <td id="LC254" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> q <span class="pl-k">in</span> qList:</td>
|
|
|
1774 </tr>
|
|
|
1775 <tr>
|
|
|
1776 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
|
|
|
1777 <td id="LC255" class="blob-code blob-code-inner js-file-line"> f_df <span class="pl-k">=</span> fpkm_df[(fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> q)]</td>
|
|
|
1778 </tr>
|
|
|
1779 <tr>
|
|
|
1780 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
|
|
|
1781 <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-c1">len</span>(f_df) <span class="pl-k">></span> <span class="pl-c1">1</span>:</td>
|
|
|
1782 </tr>
|
|
|
1783 <tr>
|
|
|
1784 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
|
|
|
1785 <td id="LC257" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">'</span>WARNING MULTIPLE FPKM<span class="pl-pds">'</span></span>)</td>
|
|
|
1786 </tr>
|
|
|
1787 <tr>
|
|
|
1788 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
|
|
|
1789 <td id="LC258" class="blob-code blob-code-inner js-file-line"> new_fpkm<span class="pl-k">=</span><span class="pl-c1">list</span>(f_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>])</td>
|
|
|
1790 </tr>
|
|
|
1791 <tr>
|
|
|
1792 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
|
|
|
1793 <td id="LC259" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> (new_fpkm[<span class="pl-c1">0</span>])</td>
|
|
|
1794 </tr>
|
|
|
1795 <tr>
|
|
|
1796 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
|
|
|
1797 <td id="LC260" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(f)</span></td>
|
|
|
1798 </tr>
|
|
|
1799 <tr>
|
|
|
1800 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
|
|
|
1801 <td id="LC261" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> new_df.append({<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>: q, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>: sv, <span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>: f}, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1802 </tr>
|
|
|
1803 <tr>
|
|
|
1804 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
|
|
|
1805 <td id="LC262" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> new_df.groupby(<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum().reset_index()</td>
|
|
|
1806 </tr>
|
|
|
1807 <tr>
|
|
|
1808 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
|
|
|
1809 <td id="LC263" class="blob-code blob-code-inner js-file-line">
|
|
|
1810 </td>
|
|
|
1811 </tr>
|
|
|
1812 <tr>
|
|
|
1813 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
|
|
|
1814 <td id="LC264" class="blob-code blob-code-inner js-file-line"> FPKMsum_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> FPKMsum_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: getPhyloNumber(row[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>]), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
|
|
|
1815 </tr>
|
|
|
1816 <tr>
|
|
|
1817 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
|
|
|
1818 <td id="LC265" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td>
|
|
|
1819 </tr>
|
|
|
1820 <tr>
|
|
|
1821 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
|
|
|
1822 <td id="LC266" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.reset_index(<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1823 </tr>
|
|
|
1824 <tr>
|
|
|
1825 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
|
|
|
1826 <td id="LC267" class="blob-code blob-code-inner js-file-line">
|
|
|
1827 </td>
|
|
|
1828 </tr>
|
|
|
1829 <tr>
|
|
|
1830 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
|
|
|
1831 <td id="LC268" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum_df)</span></td>
|
|
|
1832 </tr>
|
|
|
1833 <tr>
|
|
|
1834 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
|
|
|
1835 <td id="LC269" class="blob-code blob-code-inner js-file-line"> FPKMsum_df.to_csv(<span class="pl-s"><span class="pl-pds">'</span>FPKM_sum.csv<span class="pl-pds">'</span></span>)</td>
|
|
|
1836 </tr>
|
|
|
1837 <tr>
|
|
|
1838 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
|
|
|
1839 <td id="LC270" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum_df.groupby(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum().reset_index()</td>
|
|
|
1840 </tr>
|
|
|
1841 <tr>
|
|
|
1842 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
|
|
|
1843 <td id="LC271" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum2_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td>
|
|
|
1844 </tr>
|
|
|
1845 <tr>
|
|
|
1846 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
|
|
|
1847 <td id="LC272" class="blob-code blob-code-inner js-file-line">
|
|
|
1848 </td>
|
|
|
1849 </tr>
|
|
|
1850 <tr>
|
|
|
1851 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
|
|
|
1852 <td id="LC273" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum2_df)</span></td>
|
|
|
1853 </tr>
|
|
|
1854 <tr>
|
|
|
1855 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
|
|
|
1856 <td id="LC274" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df.to_csv(<span class="pl-s"><span class="pl-pds">'</span>FPKM_sum2.csv<span class="pl-pds">'</span></span>) <span class="pl-c"><span class="pl-c">#</span> in case more than one entry for a particular phylotype</span></td>
|
|
|
1857 </tr>
|
|
|
1858 <tr>
|
|
|
1859 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
|
|
|
1860 <td id="LC275" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> FPKMsum_df, FPKMsum2_df</td>
|
|
|
1861 </tr>
|
|
|
1862 <tr>
|
|
|
1863 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
|
|
|
1864 <td id="LC276" class="blob-code blob-code-inner js-file-line">
|
|
|
1865 </td>
|
|
|
1866 </tr>
|
|
|
1867 <tr>
|
|
|
1868 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
|
|
|
1869 <td id="LC277" class="blob-code blob-code-inner js-file-line">
|
|
|
1870 </td>
|
|
|
1871 </tr>
|
|
|
1872 <tr>
|
|
|
1873 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
|
|
|
1874 <td id="LC278" class="blob-code blob-code-inner js-file-line">
|
|
|
1875 </td>
|
|
|
1876 </tr>
|
|
|
1877 <tr>
|
|
|
1878 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
|
|
|
1879 <td id="LC279" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">normalisef</span>(<span class="pl-smi">f</span>,<span class="pl-smi">max</span>):</td>
|
|
|
1880 </tr>
|
|
|
1881 <tr>
|
|
|
1882 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
|
|
|
1883 <td id="LC280" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> f<span class="pl-k">/</span><span class="pl-c1">max</span></td>
|
|
|
1884 </tr>
|
|
|
1885 <tr>
|
|
|
1886 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
|
|
|
1887 <td id="LC281" class="blob-code blob-code-inner js-file-line">
|
|
|
1888 </td>
|
|
|
1889 </tr>
|
|
|
1890 <tr>
|
|
|
1891 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
|
|
|
1892 <td id="LC282" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getComposite_sum2</span>(<span class="pl-smi">nameList</span>,<span class="pl-smi">sum2_dfs</span>):</td>
|
|
|
1893 </tr>
|
|
|
1894 <tr>
|
|
|
1895 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
|
|
|
1896 <td id="LC283" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> lets get a composite sum2_df from all of the sum2_dfs</span></td>
|
|
|
1897 </tr>
|
|
|
1898 <tr>
|
|
|
1899 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
|
|
|
1900 <td id="LC284" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> []</td>
|
|
|
1901 </tr>
|
|
|
1902 <tr>
|
|
|
1903 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
|
|
|
1904 <td id="LC285" class="blob-code blob-code-inner js-file-line">
|
|
|
1905 </td>
|
|
|
1906 </tr>
|
|
|
1907 <tr>
|
|
|
1908 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
|
|
|
1909 <td id="LC286" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td>
|
|
|
1910 </tr>
|
|
|
1911 <tr>
|
|
|
1912 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
|
|
|
1913 <td id="LC287" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum()</td>
|
|
|
1914 </tr>
|
|
|
1915 <tr>
|
|
|
1916 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
|
|
|
1917 <td id="LC288" class="blob-code blob-code-inner js-file-line"> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_dfs[i].apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], total), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
|
|
|
1918 </tr>
|
|
|
1919 <tr>
|
|
|
1920 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
|
|
|
1921 <td id="LC289" class="blob-code blob-code-inner js-file-line"> pSeries <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td>
|
|
|
1922 </tr>
|
|
|
1923 <tr>
|
|
|
1924 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
|
|
|
1925 <td id="LC290" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pSeries:</td>
|
|
|
1926 </tr>
|
|
|
1927 <tr>
|
|
|
1928 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
|
|
|
1929 <td id="LC291" class="blob-code blob-code-inner js-file-line"> phyList.append(p) <span class="pl-c"><span class="pl-c">#</span> get all the phylotypes in this one</span></td>
|
|
|
1930 </tr>
|
|
|
1931 <tr>
|
|
|
1932 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
|
|
|
1933 <td id="LC292" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> <span class="pl-c1">list</span>(<span class="pl-c1">set</span>(phyList))</td>
|
|
|
1934 </tr>
|
|
|
1935 <tr>
|
|
|
1936 <td id="L293" class="blob-num js-line-number" data-line-number="293"></td>
|
|
|
1937 <td id="LC293" class="blob-code blob-code-inner js-file-line"> phyList.sort()</td>
|
|
|
1938 </tr>
|
|
|
1939 <tr>
|
|
|
1940 <td id="L294" class="blob-num js-line-number" data-line-number="294"></td>
|
|
|
1941 <td id="LC294" class="blob-code blob-code-inner js-file-line"> composite_sum2_df <span class="pl-k">=</span> pd.DataFrame(phyList, <span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td>
|
|
|
1942 </tr>
|
|
|
1943 <tr>
|
|
|
1944 <td id="L295" class="blob-num js-line-number" data-line-number="295"></td>
|
|
|
1945 <td id="LC295" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td>
|
|
|
1946 </tr>
|
|
|
1947 <tr>
|
|
|
1948 <td id="L296" class="blob-num js-line-number" data-line-number="296"></td>
|
|
|
1949 <td id="LC296" class="blob-code blob-code-inner js-file-line"> wList <span class="pl-k">=</span> []</td>
|
|
|
1950 </tr>
|
|
|
1951 <tr>
|
|
|
1952 <td id="L297" class="blob-num js-line-number" data-line-number="297"></td>
|
|
|
1953 <td id="LC297" class="blob-code blob-code-inner js-file-line"> pindf <span class="pl-k">=</span> <span class="pl-c1">list</span>(sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td>
|
|
|
1954 </tr>
|
|
|
1955 <tr>
|
|
|
1956 <td id="L298" class="blob-num js-line-number" data-line-number="298"></td>
|
|
|
1957 <td id="LC298" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(pindf)</span></td>
|
|
|
1958 </tr>
|
|
|
1959 <tr>
|
|
|
1960 <td id="L299" class="blob-num js-line-number" data-line-number="299"></td>
|
|
|
1961 <td id="LC299" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> phyList:</td>
|
|
|
1962 </tr>
|
|
|
1963 <tr>
|
|
|
1964 <td id="L300" class="blob-num js-line-number" data-line-number="300"></td>
|
|
|
1965 <td id="LC300" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> p <span class="pl-k">in</span> pindf:</td>
|
|
|
1966 </tr>
|
|
|
1967 <tr>
|
|
|
1968 <td id="L301" class="blob-num js-line-number" data-line-number="301"></td>
|
|
|
1969 <td id="LC301" class="blob-code blob-code-inner js-file-line"> df <span class="pl-k">=</span> sum2_dfs[i]</td>
|
|
|
1970 </tr>
|
|
|
1971 <tr>
|
|
|
1972 <td id="L302" class="blob-num js-line-number" data-line-number="302"></td>
|
|
|
1973 <td id="LC302" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> df.loc[df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> p, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>].iloc[<span class="pl-c1">0</span>]</td>
|
|
|
1974 </tr>
|
|
|
1975 <tr>
|
|
|
1976 <td id="L303" class="blob-num js-line-number" data-line-number="303"></td>
|
|
|
1977 <td id="LC303" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td>
|
|
|
1978 </tr>
|
|
|
1979 <tr>
|
|
|
1980 <td id="L304" class="blob-num js-line-number" data-line-number="304"></td>
|
|
|
1981 <td id="LC304" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1982 </tr>
|
|
|
1983 <tr>
|
|
|
1984 <td id="L305" class="blob-num js-line-number" data-line-number="305"></td>
|
|
|
1985 <td id="LC305" class="blob-code blob-code-inner js-file-line"> wList.append(w)</td>
|
|
|
1986 </tr>
|
|
|
1987 <tr>
|
|
|
1988 <td id="L306" class="blob-num js-line-number" data-line-number="306"></td>
|
|
|
1989 <td id="LC306" class="blob-code blob-code-inner js-file-line"> composite_sum2_df[nameList[i]] <span class="pl-k">=</span> wList</td>
|
|
|
1990 </tr>
|
|
|
1991 <tr>
|
|
|
1992 <td id="L307" class="blob-num js-line-number" data-line-number="307"></td>
|
|
|
1993 <td id="LC307" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(composite_sum2_df)</span></td>
|
|
|
1994 </tr>
|
|
|
1995 <tr>
|
|
|
1996 <td id="L308" class="blob-num js-line-number" data-line-number="308"></td>
|
|
|
1997 <td id="LC308" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>composite_sum2_df.to_csv('composite.csv')</span></td>
|
|
|
1998 </tr>
|
|
|
1999 <tr>
|
|
|
2000 <td id="L309" class="blob-num js-line-number" data-line-number="309"></td>
|
|
|
2001 <td id="LC309" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> composite_sum2_df</td>
|
|
|
2002 </tr>
|
|
|
2003 <tr>
|
|
|
2004 <td id="L310" class="blob-num js-line-number" data-line-number="310"></td>
|
|
|
2005 <td id="LC310" class="blob-code blob-code-inner js-file-line">
|
|
|
2006 </td>
|
|
|
2007 </tr>
|
|
|
2008 <tr>
|
|
|
2009 <td id="L311" class="blob-num js-line-number" data-line-number="311"></td>
|
|
|
2010 <td id="LC311" class="blob-code blob-code-inner js-file-line">
|
|
|
2011 </td>
|
|
|
2012 </tr>
|
|
|
2013 <tr>
|
|
|
2014 <td id="L312" class="blob-num js-line-number" data-line-number="312"></td>
|
|
|
2015 <td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doMultiBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">composite_df</span>): <span class="pl-c"><span class="pl-c">#</span>array of multiple sum2_dfs</span></td>
|
|
|
2016 </tr>
|
|
|
2017 <tr>
|
|
|
2018 <td id="L313" class="blob-num js-line-number" data-line-number="313"></td>
|
|
|
2019 <td id="LC313" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td>
|
|
|
2020 </tr>
|
|
|
2021 <tr>
|
|
|
2022 <td id="L314" class="blob-num js-line-number" data-line-number="314"></td>
|
|
|
2023 <td id="LC314" class="blob-code blob-code-inner js-file-line"> sampnum <span class="pl-k">=</span> <span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span></td>
|
|
|
2024 </tr>
|
|
|
2025 <tr>
|
|
|
2026 <td id="L315" class="blob-num js-line-number" data-line-number="315"></td>
|
|
|
2027 <td id="LC315" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> need to arrange bars</span></td>
|
|
|
2028 </tr>
|
|
|
2029 <tr>
|
|
|
2030 <td id="L316" class="blob-num js-line-number" data-line-number="316"></td>
|
|
|
2031 <td id="LC316" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> number of phylotype = len(composite_df)</span></td>
|
|
|
2032 </tr>
|
|
|
2033 <tr>
|
|
|
2034 <td id="L317" class="blob-num js-line-number" data-line-number="317"></td>
|
|
|
2035 <td id="LC317" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>number of bars = (len(labelist)-1) +1 for space</span></td>
|
|
|
2036 </tr>
|
|
|
2037 <tr>
|
|
|
2038 <td id="L318" class="blob-num js-line-number" data-line-number="318"></td>
|
|
|
2039 <td id="LC318" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> ytick needs to ne</span></td>
|
|
|
2040 </tr>
|
|
|
2041 <tr>
|
|
|
2042 <td id="L319" class="blob-num js-line-number" data-line-number="319"></td>
|
|
|
2043 <td id="LC319" class="blob-code blob-code-inner js-file-line">
|
|
|
2044 </td>
|
|
|
2045 </tr>
|
|
|
2046 <tr>
|
|
|
2047 <td id="L320" class="blob-num js-line-number" data-line-number="320"></td>
|
|
|
2048 <td id="LC320" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab10<span class="pl-pds">'</span></span>)</td>
|
|
|
2049 </tr>
|
|
|
2050 <tr>
|
|
|
2051 <td id="L321" class="blob-num js-line-number" data-line-number="321"></td>
|
|
|
2052 <td id="LC321" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td>
|
|
|
2053 </tr>
|
|
|
2054 <tr>
|
|
|
2055 <td id="L322" class="blob-num js-line-number" data-line-number="322"></td>
|
|
|
2056 <td id="LC322" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptomes. <span class="pl-pds">"</span></span> \</td>
|
|
|
2057 </tr>
|
|
|
2058 <tr>
|
|
|
2059 <td id="L323" class="blob-num js-line-number" data-line-number="323"></td>
|
|
|
2060 <td id="LC323" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">"</span></span> \</td>
|
|
|
2061 </tr>
|
|
|
2062 <tr>
|
|
|
2063 <td id="L324" class="blob-num js-line-number" data-line-number="324"></td>
|
|
|
2064 <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>for combined transcript abundance. <span class="pl-pds">"</span></span> \</td>
|
|
|
2065 </tr>
|
|
|
2066 <tr>
|
|
|
2067 <td id="L325" class="blob-num js-line-number" data-line-number="325"></td>
|
|
|
2068 <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td>
|
|
|
2069 </tr>
|
|
|
2070 <tr>
|
|
|
2071 <td id="L326" class="blob-num js-line-number" data-line-number="326"></td>
|
|
|
2072 <td id="LC326" class="blob-code blob-code-inner js-file-line"> width <span class="pl-k">=</span> <span class="pl-c1">0.6</span></td>
|
|
|
2073 </tr>
|
|
|
2074 <tr>
|
|
|
2075 <td id="L327" class="blob-num js-line-number" data-line-number="327"></td>
|
|
|
2076 <td id="LC327" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> np.arange(width<span class="pl-k">*</span>sampnum<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>))</td>
|
|
|
2077 </tr>
|
|
|
2078 <tr>
|
|
|
2079 <td id="L328" class="blob-num js-line-number" data-line-number="328"></td>
|
|
|
2080 <td id="LC328" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(ind)</span></td>
|
|
|
2081 </tr>
|
|
|
2082 <tr>
|
|
|
2083 <td id="L329" class="blob-num js-line-number" data-line-number="329"></td>
|
|
|
2084 <td id="LC329" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span><span class="pl-c1">0.4</span></td>
|
|
|
2085 </tr>
|
|
|
2086 <tr>
|
|
|
2087 <td id="L330" class="blob-num js-line-number" data-line-number="330"></td>
|
|
|
2088 <td id="LC330" class="blob-code blob-code-inner js-file-line">
|
|
|
2089 </td>
|
|
|
2090 </tr>
|
|
|
2091 <tr>
|
|
|
2092 <td id="L331" class="blob-num js-line-number" data-line-number="331"></td>
|
|
|
2093 <td id="LC331" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td>
|
|
|
2094 </tr>
|
|
|
2095 <tr>
|
|
|
2096 <td id="L332" class="blob-num js-line-number" data-line-number="332"></td>
|
|
|
2097 <td id="LC332" class="blob-code blob-code-inner js-file-line">
|
|
|
2098 </td>
|
|
|
2099 </tr>
|
|
|
2100 <tr>
|
|
|
2101 <td id="L333" class="blob-num js-line-number" data-line-number="333"></td>
|
|
|
2102 <td id="LC333" class="blob-code blob-code-inner js-file-line">
|
|
|
2103 </td>
|
|
|
2104 </tr>
|
|
|
2105 <tr>
|
|
|
2106 <td id="L334" class="blob-num js-line-number" data-line-number="334"></td>
|
|
|
2107 <td id="LC334" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> s <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>, <span class="pl-c1">len</span>(labelList)):</td>
|
|
|
2108 </tr>
|
|
|
2109 <tr>
|
|
|
2110 <td id="L335" class="blob-num js-line-number" data-line-number="335"></td>
|
|
|
2111 <td id="LC335" class="blob-code blob-code-inner js-file-line"> ax.barh(ind, composite_df[labelList[s]], width, <span class="pl-v">color</span><span class="pl-k">=</span>palette[s], <span class="pl-v">label</span><span class="pl-k">=</span>labelList[s])</td>
|
|
|
2112 </tr>
|
|
|
2113 <tr>
|
|
|
2114 <td id="L336" class="blob-num js-line-number" data-line-number="336"></td>
|
|
|
2115 <td id="LC336" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> ind <span class="pl-k">+</span> width</td>
|
|
|
2116 </tr>
|
|
|
2117 <tr>
|
|
|
2118 <td id="L337" class="blob-num js-line-number" data-line-number="337"></td>
|
|
|
2119 <td id="LC337" class="blob-code blob-code-inner js-file-line">
|
|
|
2120 </td>
|
|
|
2121 </tr>
|
|
|
2122 <tr>
|
|
|
2123 <td id="L338" class="blob-num js-line-number" data-line-number="338"></td>
|
|
|
2124 <td id="LC338" class="blob-code blob-code-inner js-file-line"> ax.set(<span class="pl-v">yticks</span><span class="pl-k">=</span>np.arange(width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">2</span>)<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>)), <span class="pl-v">yticklabels</span><span class="pl-k">=</span>composite_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span> , ylim=[(len(labelList)-1) * width - 1, len(composite_df)])</span></td>
|
|
|
2125 </tr>
|
|
|
2126 <tr>
|
|
|
2127 <td id="L339" class="blob-num js-line-number" data-line-number="339"></td>
|
|
|
2128 <td id="LC339" class="blob-code blob-code-inner js-file-line"> ax.legend()</td>
|
|
|
2129 </tr>
|
|
|
2130 <tr>
|
|
|
2131 <td id="L340" class="blob-num js-line-number" data-line-number="340"></td>
|
|
|
2132 <td id="LC340" class="blob-code blob-code-inner js-file-line">
|
|
|
2133 </td>
|
|
|
2134 </tr>
|
|
|
2135 <tr>
|
|
|
2136 <td id="L341" class="blob-num js-line-number" data-line-number="341"></td>
|
|
|
2137 <td id="LC341" class="blob-code blob-code-inner js-file-line">
|
|
|
2138 </td>
|
|
|
2139 </tr>
|
|
|
2140 <tr>
|
|
|
2141 <td id="L342" class="blob-num js-line-number" data-line-number="342"></td>
|
|
|
2142 <td id="LC342" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)</td>
|
|
|
2143 </tr>
|
|
|
2144 <tr>
|
|
|
2145 <td id="L343" class="blob-num js-line-number" data-line-number="343"></td>
|
|
|
2146 <td id="LC343" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td>
|
|
|
2147 </tr>
|
|
|
2148 <tr>
|
|
|
2149 <td id="L344" class="blob-num js-line-number" data-line-number="344"></td>
|
|
|
2150 <td id="LC344" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">'</span>Weighted Phylotype Frequency<span class="pl-pds">'</span></span>)</td>
|
|
|
2151 </tr>
|
|
|
2152 <tr>
|
|
|
2153 <td id="L345" class="blob-num js-line-number" data-line-number="345"></td>
|
|
|
2154 <td id="LC345" class="blob-code blob-code-inner js-file-line">
|
|
|
2155 </td>
|
|
|
2156 </tr>
|
|
|
2157 <tr>
|
|
|
2158 <td id="L346" class="blob-num js-line-number" data-line-number="346"></td>
|
|
|
2159 <td id="LC346" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va="top", wrap="True")</span></td>
|
|
|
2160 </tr>
|
|
|
2161 <tr>
|
|
|
2162 <td id="L347" class="blob-num js-line-number" data-line-number="347"></td>
|
|
|
2163 <td id="LC347" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td>
|
|
|
2164 </tr>
|
|
|
2165 <tr>
|
|
|
2166 <td id="L348" class="blob-num js-line-number" data-line-number="348"></td>
|
|
|
2167 <td id="LC348" class="blob-code blob-code-inner js-file-line">
|
|
|
2168 </td>
|
|
|
2169 </tr>
|
|
|
2170 <tr>
|
|
|
2171 <td id="L349" class="blob-num js-line-number" data-line-number="349"></td>
|
|
|
2172 <td id="LC349" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.92</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td>
|
|
|
2173 </tr>
|
|
|
2174 <tr>
|
|
|
2175 <td id="L350" class="blob-num js-line-number" data-line-number="350"></td>
|
|
|
2176 <td id="LC350" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>True<span class="pl-pds">'</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>left<span class="pl-pds">'</span></span>,)</td>
|
|
|
2177 </tr>
|
|
|
2178 <tr>
|
|
|
2179 <td id="L351" class="blob-num js-line-number" data-line-number="351"></td>
|
|
|
2180 <td id="LC351" class="blob-code blob-code-inner js-file-line">
|
|
|
2181 </td>
|
|
|
2182 </tr>
|
|
|
2183 <tr>
|
|
|
2184 <td id="L352" class="blob-num js-line-number" data-line-number="352"></td>
|
|
|
2185 <td id="LC352" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png<span class="pl-pds">"</span></span>)</td>
|
|
|
2186 </tr>
|
|
|
2187 <tr>
|
|
|
2188 <td id="L353" class="blob-num js-line-number" data-line-number="353"></td>
|
|
|
2189 <td id="LC353" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td>
|
|
|
2190 </tr>
|
|
|
2191 <tr>
|
|
|
2192 <td id="L354" class="blob-num js-line-number" data-line-number="354"></td>
|
|
|
2193 <td id="LC354" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>phylotypes.pdf<span class="pl-pds">"</span></span>)</td>
|
|
|
2194 </tr>
|
|
|
2195 <tr>
|
|
|
2196 <td id="L355" class="blob-num js-line-number" data-line-number="355"></td>
|
|
|
2197 <td id="LC355" class="blob-code blob-code-inner js-file-line"> plt.show()</td>
|
|
|
2198 </tr>
|
|
|
2199 <tr>
|
|
|
2200 <td id="L356" class="blob-num js-line-number" data-line-number="356"></td>
|
|
|
2201 <td id="LC356" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td>
|
|
|
2202 </tr>
|
|
|
2203 <tr>
|
|
|
2204 <td id="L357" class="blob-num js-line-number" data-line-number="357"></td>
|
|
|
2205 <td id="LC357" class="blob-code blob-code-inner js-file-line">
|
|
|
2206 </td>
|
|
|
2207 </tr>
|
|
|
2208 <tr>
|
|
|
2209 <td id="L358" class="blob-num js-line-number" data-line-number="358"></td>
|
|
|
2210 <td id="LC358" class="blob-code blob-code-inner js-file-line">
|
|
|
2211 </td>
|
|
|
2212 </tr>
|
|
|
2213 <tr>
|
|
|
2214 <td id="L359" class="blob-num js-line-number" data-line-number="359"></td>
|
|
|
2215 <td id="LC359" class="blob-code blob-code-inner js-file-line">
|
|
|
2216 </td>
|
|
|
2217 </tr>
|
|
|
2218 <tr>
|
|
|
2219 <td id="L360" class="blob-num js-line-number" data-line-number="360"></td>
|
|
|
2220 <td id="LC360" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">sum2_df</span>):</td>
|
|
|
2221 </tr>
|
|
|
2222 <tr>
|
|
|
2223 <td id="L361" class="blob-num js-line-number" data-line-number="361"></td>
|
|
|
2224 <td id="LC361" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab20<span class="pl-pds">'</span></span>)</td>
|
|
|
2225 </tr>
|
|
|
2226 <tr>
|
|
|
2227 <td id="L362" class="blob-num js-line-number" data-line-number="362"></td>
|
|
|
2228 <td id="LC362" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td>
|
|
|
2229 </tr>
|
|
|
2230 <tr>
|
|
|
2231 <td id="L363" class="blob-num js-line-number" data-line-number="363"></td>
|
|
|
2232 <td id="LC363" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptome. <span class="pl-pds">"</span></span> \</td>
|
|
|
2233 </tr>
|
|
|
2234 <tr>
|
|
|
2235 <td id="L364" class="blob-num js-line-number" data-line-number="364"></td>
|
|
|
2236 <td id="LC364" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">"</span></span> \</td>
|
|
|
2237 </tr>
|
|
|
2238 <tr>
|
|
|
2239 <td id="L365" class="blob-num js-line-number" data-line-number="365"></td>
|
|
|
2240 <td id="LC365" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>for combined transcript abundance. <span class="pl-pds">"</span></span> \</td>
|
|
|
2241 </tr>
|
|
|
2242 <tr>
|
|
|
2243 <td id="L366" class="blob-num js-line-number" data-line-number="366"></td>
|
|
|
2244 <td id="LC366" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td>
|
|
|
2245 </tr>
|
|
|
2246 <tr>
|
|
|
2247 <td id="L367" class="blob-num js-line-number" data-line-number="367"></td>
|
|
|
2248 <td id="LC367" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get a list of phylotype, create equivalent of saccver, get a list of</span></td>
|
|
|
2249 </tr>
|
|
|
2250 <tr>
|
|
|
2251 <td id="L368" class="blob-num js-line-number" data-line-number="368"></td>
|
|
|
2252 <td id="LC368" class="blob-code blob-code-inner js-file-line"> maxFPKM <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].max()</td>
|
|
|
2253 </tr>
|
|
|
2254 <tr>
|
|
|
2255 <td id="L369" class="blob-num js-line-number" data-line-number="369"></td>
|
|
|
2256 <td id="LC369" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum()</td>
|
|
|
2257 </tr>
|
|
|
2258 <tr>
|
|
|
2259 <td id="L370" class="blob-num js-line-number" data-line-number="370"></td>
|
|
|
2260 <td id="LC370" class="blob-code blob-code-inner js-file-line">
|
|
|
2261 </td>
|
|
|
2262 </tr>
|
|
|
2263 <tr>
|
|
|
2264 <td id="L371" class="blob-num js-line-number" data-line-number="371"></td>
|
|
|
2265 <td id="LC371" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Normalised<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], maxFPKM),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
|
|
|
2266 </tr>
|
|
|
2267 <tr>
|
|
|
2268 <td id="L372" class="blob-num js-line-number" data-line-number="372"></td>
|
|
|
2269 <td id="LC372" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Weighted<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], total),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
|
|
|
2270 </tr>
|
|
|
2271 <tr>
|
|
|
2272 <td id="L373" class="blob-num js-line-number" data-line-number="373"></td>
|
|
|
2273 <td id="LC373" class="blob-code blob-code-inner js-file-line"> pList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td>
|
|
|
2274 </tr>
|
|
|
2275 <tr>
|
|
|
2276 <td id="L374" class="blob-num js-line-number" data-line-number="374"></td>
|
|
|
2277 <td id="LC374" class="blob-code blob-code-inner js-file-line"> phList <span class="pl-k">=</span> []</td>
|
|
|
2278 </tr>
|
|
|
2279 <tr>
|
|
|
2280 <td id="L375" class="blob-num js-line-number" data-line-number="375"></td>
|
|
|
2281 <td id="LC375" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pList:</td>
|
|
|
2282 </tr>
|
|
|
2283 <tr>
|
|
|
2284 <td id="L376" class="blob-num js-line-number" data-line-number="376"></td>
|
|
|
2285 <td id="LC376" class="blob-code blob-code-inner js-file-line"> phList.append(<span class="pl-c1">str</span>(p))</td>
|
|
|
2286 </tr>
|
|
|
2287 <tr>
|
|
|
2288 <td id="L377" class="blob-num js-line-number" data-line-number="377"></td>
|
|
|
2289 <td id="LC377" class="blob-code blob-code-inner js-file-line">
|
|
|
2290 </td>
|
|
|
2291 </tr>
|
|
|
2292 <tr>
|
|
|
2293 <td id="L378" class="blob-num js-line-number" data-line-number="378"></td>
|
|
|
2294 <td id="LC378" class="blob-code blob-code-inner js-file-line"> fList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Weighted<span class="pl-pds">'</span></span>]</td>
|
|
|
2295 </tr>
|
|
|
2296 <tr>
|
|
|
2297 <td id="L379" class="blob-num js-line-number" data-line-number="379"></td>
|
|
|
2298 <td id="LC379" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(phList)<span class="pl-k">*</span><span class="pl-c1">0.3</span></td>
|
|
|
2299 </tr>
|
|
|
2300 <tr>
|
|
|
2301 <td id="L380" class="blob-num js-line-number" data-line-number="380"></td>
|
|
|
2302 <td id="LC380" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td>
|
|
|
2303 </tr>
|
|
|
2304 <tr>
|
|
|
2305 <td id="L381" class="blob-num js-line-number" data-line-number="381"></td>
|
|
|
2306 <td id="LC381" class="blob-code blob-code-inner js-file-line">
|
|
|
2307 </td>
|
|
|
2308 </tr>
|
|
|
2309 <tr>
|
|
|
2310 <td id="L382" class="blob-num js-line-number" data-line-number="382"></td>
|
|
|
2311 <td id="LC382" class="blob-code blob-code-inner js-file-line"> ax.barh(phList, fList, <span class="pl-v">color</span><span class="pl-k">=</span>palette)</td>
|
|
|
2312 </tr>
|
|
|
2313 <tr>
|
|
|
2314 <td id="L383" class="blob-num js-line-number" data-line-number="383"></td>
|
|
|
2315 <td id="LC383" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)</td>
|
|
|
2316 </tr>
|
|
|
2317 <tr>
|
|
|
2318 <td id="L384" class="blob-num js-line-number" data-line-number="384"></td>
|
|
|
2319 <td id="LC384" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td>
|
|
|
2320 </tr>
|
|
|
2321 <tr>
|
|
|
2322 <td id="L385" class="blob-num js-line-number" data-line-number="385"></td>
|
|
|
2323 <td id="LC385" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">'</span>Weighted Phylotype Frequency<span class="pl-pds">'</span></span>)</td>
|
|
|
2324 </tr>
|
|
|
2325 <tr>
|
|
|
2326 <td id="L386" class="blob-num js-line-number" data-line-number="386"></td>
|
|
|
2327 <td id="LC386" class="blob-code blob-code-inner js-file-line">
|
|
|
2328 </td>
|
|
|
2329 </tr>
|
|
|
2330 <tr>
|
|
|
2331 <td id="L387" class="blob-num js-line-number" data-line-number="387"></td>
|
|
|
2332 <td id="LC387" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va="top", wrap="True")</span></td>
|
|
|
2333 </tr>
|
|
|
2334 <tr>
|
|
|
2335 <td id="L388" class="blob-num js-line-number" data-line-number="388"></td>
|
|
|
2336 <td id="LC388" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td>
|
|
|
2337 </tr>
|
|
|
2338 <tr>
|
|
|
2339 <td id="L389" class="blob-num js-line-number" data-line-number="389"></td>
|
|
|
2340 <td id="LC389" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td>
|
|
|
2341 </tr>
|
|
|
2342 <tr>
|
|
|
2343 <td id="L390" class="blob-num js-line-number" data-line-number="390"></td>
|
|
|
2344 <td id="LC390" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>True<span class="pl-pds">'</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>left<span class="pl-pds">'</span></span>,)</td>
|
|
|
2345 </tr>
|
|
|
2346 <tr>
|
|
|
2347 <td id="L391" class="blob-num js-line-number" data-line-number="391"></td>
|
|
|
2348 <td id="LC391" class="blob-code blob-code-inner js-file-line">
|
|
|
2349 </td>
|
|
|
2350 </tr>
|
|
|
2351 <tr>
|
|
|
2352 <td id="L392" class="blob-num js-line-number" data-line-number="392"></td>
|
|
|
2353 <td id="LC392" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png<span class="pl-pds">"</span></span>)</td>
|
|
|
2354 </tr>
|
|
|
2355 <tr>
|
|
|
2356 <td id="L393" class="blob-num js-line-number" data-line-number="393"></td>
|
|
|
2357 <td id="LC393" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td>
|
|
|
2358 </tr>
|
|
|
2359 <tr>
|
|
|
2360 <td id="L394" class="blob-num js-line-number" data-line-number="394"></td>
|
|
|
2361 <td id="LC394" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>phylotypes.pdf<span class="pl-pds">"</span></span>)</td>
|
|
|
2362 </tr>
|
|
|
2363 <tr>
|
|
|
2364 <td id="L395" class="blob-num js-line-number" data-line-number="395"></td>
|
|
|
2365 <td id="LC395" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.show()</span></td>
|
|
|
2366 </tr>
|
|
|
2367 <tr>
|
|
|
2368 <td id="L396" class="blob-num js-line-number" data-line-number="396"></td>
|
|
|
2369 <td id="LC396" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td>
|
|
|
2370 </tr>
|
|
|
2371 <tr>
|
|
|
2372 <td id="L397" class="blob-num js-line-number" data-line-number="397"></td>
|
|
|
2373 <td id="LC397" class="blob-code blob-code-inner js-file-line">
|
|
|
2374 </td>
|
|
|
2375 </tr>
|
|
|
2376 <tr>
|
|
|
2377 <td id="L398" class="blob-num js-line-number" data-line-number="398"></td>
|
|
|
2378 <td id="LC398" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}</span></td>
|
|
|
2379 </tr>
|
|
|
2380 <tr>
|
|
|
2381 <td id="L399" class="blob-num js-line-number" data-line-number="399"></td>
|
|
|
2382 <td id="LC399" class="blob-code blob-code-inner js-file-line">
|
|
|
2383 </td>
|
|
|
2384 </tr>
|
|
|
2385 <tr>
|
|
|
2386 <td id="L400" class="blob-num js-line-number" data-line-number="400"></td>
|
|
|
2387 <td id="LC400" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptomicProcess</span>(<span class="pl-smi">args</span>,<span class="pl-smi">argdict</span>):</td>
|
|
|
2388 </tr>
|
|
|
2389 <tr>
|
|
|
2390 <td id="L401" class="blob-num js-line-number" data-line-number="401"></td>
|
|
|
2391 <td id="LC401" class="blob-code blob-code-inner js-file-line"> tdict <span class="pl-k">=</span> {}</td>
|
|
|
2392 </tr>
|
|
|
2393 <tr>
|
|
|
2394 <td id="L402" class="blob-num js-line-number" data-line-number="402"></td>
|
|
|
2395 <td id="LC402" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]</td>
|
|
|
2396 </tr>
|
|
|
2397 <tr>
|
|
|
2398 <td id="L403" class="blob-num js-line-number" data-line-number="403"></td>
|
|
|
2399 <td id="LC403" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>]]</td>
|
|
|
2400 </tr>
|
|
|
2401 <tr>
|
|
|
2402 <td id="L404" class="blob-num js-line-number" data-line-number="404"></td>
|
|
|
2403 <td id="LC404" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>]]</td>
|
|
|
2404 </tr>
|
|
|
2405 <tr>
|
|
|
2406 <td id="L405" class="blob-num js-line-number" data-line-number="405"></td>
|
|
|
2407 <td id="LC405" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]]</td>
|
|
|
2408 </tr>
|
|
|
2409 <tr>
|
|
|
2410 <td id="L406" class="blob-num js-line-number" data-line-number="406"></td>
|
|
|
2411 <td id="LC406" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>vivax_trans_database<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">'</span></span></td>
|
|
|
2412 </tr>
|
|
|
2413 <tr>
|
|
|
2414 <td id="L407" class="blob-num js-line-number" data-line-number="407"></td>
|
|
|
2415 <td id="LC407" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]]</td>
|
|
|
2416 </tr>
|
|
|
2417 <tr>
|
|
|
2418 <td id="L408" class="blob-num js-line-number" data-line-number="408"></td>
|
|
|
2419 <td id="LC408" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]]</td>
|
|
|
2420 </tr>
|
|
|
2421 <tr>
|
|
|
2422 <td id="L409" class="blob-num js-line-number" data-line-number="409"></td>
|
|
|
2423 <td id="LC409" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]</td>
|
|
|
2424 </tr>
|
|
|
2425 <tr>
|
|
|
2426 <td id="L410" class="blob-num js-line-number" data-line-number="410"></td>
|
|
|
2427 <td id="LC410" class="blob-code blob-code-inner js-file-line"> </td>
|
|
|
2428 </tr>
|
|
|
2429 <tr>
|
|
|
2430 <td id="L411" class="blob-num js-line-number" data-line-number="411"></td>
|
|
|
2431 <td id="LC411" class="blob-code blob-code-inner js-file-line"> uploadUserReferenceFastq(tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>])</td>
|
|
|
2432 </tr>
|
|
|
2433 <tr>
|
|
|
2434 <td id="L412" class="blob-num js-line-number" data-line-number="412"></td>
|
|
|
2435 <td id="LC412" class="blob-code blob-code-inner js-file-line"> transcriptMapping(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses bowtie</span></td>
|
|
|
2436 </tr>
|
|
|
2437 <tr>
|
|
|
2438 <td id="L413" class="blob-num js-line-number" data-line-number="413"></td>
|
|
|
2439 <td id="LC413" class="blob-code blob-code-inner js-file-line"> processSamFiles(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses samtools</span></td>
|
|
|
2440 </tr>
|
|
|
2441 <tr>
|
|
|
2442 <td id="L414" class="blob-num js-line-number" data-line-number="414"></td>
|
|
|
2443 <td id="LC414" class="blob-code blob-code-inner js-file-line"> transcriptAbundance(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -> ?.cuff/*.*</span></td>
|
|
|
2444 </tr>
|
|
|
2445 <tr>
|
|
|
2446 <td id="L415" class="blob-num js-line-number" data-line-number="415"></td>
|
|
|
2447 <td id="LC415" class="blob-code blob-code-inner js-file-line"> transcriptsForBlast(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>creates name+4blast.fa</span></td>
|
|
|
2448 </tr>
|
|
|
2449 <tr>
|
|
|
2450 <td id="L416" class="blob-num js-line-number" data-line-number="416"></td>
|
|
|
2451 <td id="LC416" class="blob-code blob-code-inner js-file-line"> blastContigs(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">'</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">'</span></span>)</td>
|
|
|
2452 </tr>
|
|
|
2453 <tr>
|
|
|
2454 <td id="L417" class="blob-num js-line-number" data-line-number="417"></td>
|
|
|
2455 <td id="LC417" class="blob-code blob-code-inner js-file-line"> sum_df, sum2_df <span class="pl-k">=</span> combineFPMK(tdict)</td>
|
|
|
2456 </tr>
|
|
|
2457 <tr>
|
|
|
2458 <td id="L418" class="blob-num js-line-number" data-line-number="418"></td>
|
|
|
2459 <td id="LC418" class="blob-code blob-code-inner js-file-line"> doBarChart(tdict, sum2_df)</td>
|
|
|
2460 </tr>
|
|
|
2461 <tr>
|
|
|
2462 <td id="L419" class="blob-num js-line-number" data-line-number="419"></td>
|
|
|
2463 <td id="LC419" class="blob-code blob-code-inner js-file-line"> createHTML(tdict, sum_df)</td>
|
|
|
2464 </tr>
|
|
|
2465 <tr>
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2466 <td id="L420" class="blob-num js-line-number" data-line-number="420"></td>
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2467 <td id="LC420" class="blob-code blob-code-inner js-file-line">
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2468 </td>
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2469 </tr>
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2470 <tr>
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2471 <td id="L421" class="blob-num js-line-number" data-line-number="421"></td>
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2472 <td id="LC421" class="blob-code blob-code-inner js-file-line">
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2473 </td>
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2474 </tr>
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2475 <tr>
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2476 <td id="L422" class="blob-num js-line-number" data-line-number="422"></td>
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2477 <td id="LC422" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>__main__<span class="pl-pds">"</span></span>:</td>
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2478 </tr>
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2479 <tr>
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2480 <td id="L423" class="blob-num js-line-number" data-line-number="423"></td>
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2481 <td id="LC423" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">exit</span>()</td>
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2482 </tr>
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2483 <tr>
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2484 <td id="L424" class="blob-num js-line-number" data-line-number="424"></td>
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2485 <td id="LC424" class="blob-code blob-code-inner js-file-line">
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2486 </td>
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2487 </tr>
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2488 <tr>
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2489 <td id="L425" class="blob-num js-line-number" data-line-number="425"></td>
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2490 <td id="LC425" class="blob-code blob-code-inner js-file-line">
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2491 </td>
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2492 </tr>
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2493 </table>
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2494
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2495 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
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2496 <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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2497 <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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2498 </summary>
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2499 <details-menu>
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2500 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
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2501 <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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2502 <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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2503 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/johnheap/VAPPER-Galaxy/blame/a4e16d71fe985f389930c02f94354b87d3aabadb/Tryp_V_T.py">View git blame</a></li>
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2504 <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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2505 </ul>
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2506 </details-menu>
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2507 </details>
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2508
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2509 </div>
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2510
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2511 </div>
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2512
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2513
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2514
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2515 <details class="details-reset details-overlay details-overlay-dark">
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2516 <summary data-hotkey="l" aria-label="Jump to line"></summary>
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2517 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
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2518 <!-- '"` --><!-- </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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2519 <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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2520 <button type="submit" class="btn" data-close-dialog>Go</button>
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2521 </form> </details-dialog>
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2522 </details>
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2523
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2524
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2525
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2526 </div>
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2527 <div class="modal-backdrop js-touch-events"></div>
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2528 </div>
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2529
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2530 </main>
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2531 </div>
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2532
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2533
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2534 </div>
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2535
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2536
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2537 <div class="footer container-lg width-full p-responsive" role="contentinfo">
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2538 <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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2539 <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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2540 <li class="mr-3 mr-lg-0">© 2019 <span title="0.75142s from unicorn-74746df85b-zvhqz">GitHub</span>, Inc.</li>
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2543 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to security, text:security" href="https://github.com/security">Security</a></li>
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2545 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
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2547
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2548 <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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2549 <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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2550 </a>
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2551 <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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2552 <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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2553 <li class="mr-3 mr-lg-0"><a href="https://github.com/pricing" data-ga-click="Footer, go to Pricing, text:Pricing">Pricing</a></li>
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2554 <li class="mr-3 mr-lg-0"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
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2558
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2559 </ul>
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2560 </div>
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2561 <div class="d-flex flex-justify-center pb-6">
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|
2562 <span class="f6 text-gray-light"></span>
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2563 </div>
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2564 </div>
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2565
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2566
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2567
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2568 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
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|
2569 <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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2570 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
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|
2571 <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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|
2572 </button>
|
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|
2573 You can’t perform that action at this time.
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2574 </div>
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2575
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2576
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|
2577 <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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2578 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
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2579
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2580 <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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2581
|
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|
2582
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2583
|
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|
2584 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
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|
2585 >
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|
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2586 <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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2587 <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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2588 <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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2589 </div>
|
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|
2590 <template id="site-details-dialog">
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|
2591 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
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|
2592 <summary role="button" aria-label="Close dialog"></summary>
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|
2593 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
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2594 <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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2595 <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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2596 </button>
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|
2597 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
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2598 </details-dialog>
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2599 </details>
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|
2600 </template>
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2601
|
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|
2602 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
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2603 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
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2604 </div>
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2605 </div>
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2606
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|
2607 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
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2608
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|
2609 </body>
|
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|
2610 </html>
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2611
|
