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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=aIF6VlsMjmBGKiH9gFW0N7Dd6tKGBfaVG4YIMScDT9WHVDbYUTh6gnqmb9yMT8saP+1TzsRaVWx++i39m514Bw=="
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279 spellcheck="false"
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280 autocomplete="off"
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281 >
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282 <input type="hidden" class="js-site-search-type-field" name="type" >
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283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
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284
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|
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285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
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286
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287 <ul class="d-none js-jump-to-suggestions-template-container">
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288
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289
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290 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option">
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291 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
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292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
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293 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
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294 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
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295 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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296 </div>
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297
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298 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
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299
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|
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300 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
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|
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301 </div>
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302
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|
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303 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
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304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
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305 In this repository
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306 </span>
|
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307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
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308 All GitHub
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309 </span>
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310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
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311 </div>
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312
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|
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313 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
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314 Jump to
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315 <span class="d-inline-block ml-1 v-align-middle">↵</span>
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316 </div>
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317 </a>
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318 </li>
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319
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320 </ul>
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321
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322 <ul class="d-none js-jump-to-no-results-template-container">
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323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2">
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324 <span class="text-gray">No suggested jump to results</span>
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325 </li>
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326 </ul>
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327
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328 <ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container">
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|
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329
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|
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330
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331 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option">
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|
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332 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
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333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
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334 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
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335 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
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336 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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337 </div>
|
|
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338
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|
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339 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
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|
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340
|
|
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341 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
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|
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342 </div>
|
|
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343
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|
|
344 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
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|
|
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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|
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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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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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715
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717
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719 <tr>
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720 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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721 <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">"""</span></span></td>
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722 </tr>
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723 <tr>
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724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td>
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726 </tr>
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727 <tr>
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728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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729 <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author: John Heap, Computational Biology Facility, UoL</span></td>
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730 </tr>
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731 <tr>
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732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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733 <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td>
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734 </tr>
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735 <tr>
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737 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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738 </tr>
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739 <tr>
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740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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741 <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the "License");</span></td>
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742 </tr>
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743 <tr>
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744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
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745 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td>
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746 </tr>
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747 <tr>
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749 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td>
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750 </tr>
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751 <tr>
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757 <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td>
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758 </tr>
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759 <tr>
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760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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762 </tr>
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763 <tr>
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764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
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765 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td>
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766 </tr>
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767 <tr>
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768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
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769 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td>
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770 </tr>
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771 <tr>
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772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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773 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td>
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774 </tr>
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775 <tr>
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776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
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777 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td>
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778 </tr>
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779 <tr>
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780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
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781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td>
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782 </tr>
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783 <tr>
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784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
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785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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786 </tr>
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788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
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789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td>
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799 </td>
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802 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
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803 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td>
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804 </tr>
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805 <tr>
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806 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
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807 <td id="LC22" 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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808 </tr>
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809 <tr>
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811 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</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> os</td>
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816 </tr>
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817 <tr>
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819 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
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820 </tr>
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821 <tr>
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823 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib <span class="pl-k">as</span> mpl</td>
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824 </tr>
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825 <tr>
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827 <td id="LC27" class="blob-code blob-code-inner js-file-line">mpl.use(<span class="pl-s"><span class="pl-pds">'</span>Agg<span class="pl-pds">'</span></span>)</td>
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828 </tr>
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829 <tr>
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831 <td id="LC28" 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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832 </tr>
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833 <tr>
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840 <td id="LC30" class="blob-code blob-code-inner js-file-line">pList <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>P1<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P2<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P3<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P4<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P5<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P6<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P7<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P8<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P9<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P10<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P11<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P12<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P13<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P14<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P15<span class="pl-pds">'</span></span>]</td>
|
|
|
841 </tr>
|
|
|
842 <tr>
|
|
|
843 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
|
|
|
844 <td id="LC31" class="blob-code blob-code-inner js-file-line">quietString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span>"">> Vap_log.txt 2>&1"</span></td>
|
|
|
845 </tr>
|
|
|
846 <tr>
|
|
|
847 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
|
|
|
848 <td id="LC32" 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">strain</span>, <span class="pl-smi">forwardFN</span>,<span class="pl-smi">reverseFN</span>):</td>
|
|
|
849 </tr>
|
|
|
850 <tr>
|
|
|
851 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
|
|
|
852 <td id="LC33" 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>
|
|
|
853 </tr>
|
|
|
854 <tr>
|
|
|
855 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
|
|
|
856 <td id="LC34" 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>
|
|
|
857 </tr>
|
|
|
858 <tr>
|
|
|
859 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
|
|
|
860 <td id="LC35" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/data/Reference/Tc148<span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span>default</span></td>
|
|
|
861 </tr>
|
|
|
862 <tr>
|
|
|
863 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
|
|
|
864 <td id="LC36" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td>
|
|
|
865 </tr>
|
|
|
866 <tr>
|
|
|
867 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
|
|
|
868 <td id="LC37" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/data/Reference/Tc148<span class="pl-pds">"</span></span></td>
|
|
|
869 </tr>
|
|
|
870 <tr>
|
|
|
871 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
|
|
|
872 <td id="LC38" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td>
|
|
|
873 </tr>
|
|
|
874 <tr>
|
|
|
875 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
|
|
|
876 <td id="LC39" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/data/Reference/IL3000<span class="pl-pds">"</span></span></td>
|
|
|
877 </tr>
|
|
|
878 <tr>
|
|
|
879 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
|
|
|
880 <td id="LC40" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "bowtie2 -x Refe4rence/IL3000 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt</span></td>
|
|
|
881 </tr>
|
|
|
882 <tr>
|
|
|
883 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
|
|
|
884 <td id="LC41" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "bowtie2 -x Reference/Tc148 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt</span></td>
|
|
|
885 </tr>
|
|
|
886 <tr>
|
|
|
887 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
|
|
|
888 <td id="LC42" 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><span class="pl-k">+</span>quietString <span class="pl-c"><span class="pl-c">#</span>>log.txt</span></td>
|
|
|
889 </tr>
|
|
|
890 <tr>
|
|
|
891 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
|
|
|
892 <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(argString)</span></td>
|
|
|
893 </tr>
|
|
|
894 <tr>
|
|
|
895 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
|
|
|
896 <td id="LC44" 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>
|
|
|
897 </tr>
|
|
|
898 <tr>
|
|
|
899 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
|
|
|
900 <td id="LC45" class="blob-code blob-code-inner js-file-line">
|
|
|
901 </td>
|
|
|
902 </tr>
|
|
|
903 <tr>
|
|
|
904 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
|
|
|
905 <td id="LC46" 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>
|
|
|
906 </tr>
|
|
|
907 <tr>
|
|
|
908 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
|
|
|
909 <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>debug use a mapping sam file we have already found</span></td>
|
|
|
910 </tr>
|
|
|
911 <tr>
|
|
|
912 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
|
|
|
913 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>dir_path = os.path.dirname(os.path.realpath(__file__))</span></td>
|
|
|
914 </tr>
|
|
|
915 <tr>
|
|
|
916 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
|
|
|
917 <td id="LC49" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>bugName = dir_path+"/data/T_Test" #defasult</span></td>
|
|
|
918 </tr>
|
|
|
919 <tr>
|
|
|
920 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
|
|
|
921 <td id="LC50" class="blob-code blob-code-inner js-file-line">
|
|
|
922 </td>
|
|
|
923 </tr>
|
|
|
924 <tr>
|
|
|
925 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
|
|
|
926 <td id="LC51" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td>
|
|
|
927 </tr>
|
|
|
928 <tr>
|
|
|
929 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
|
|
|
930 <td id="LC52" 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>
|
|
|
931 </tr>
|
|
|
932 <tr>
|
|
|
933 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
|
|
|
934 <td id="LC53" class="blob-code blob-code-inner js-file-line">
|
|
|
935 </td>
|
|
|
936 </tr>
|
|
|
937 <tr>
|
|
|
938 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
|
|
|
939 <td id="LC54" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "samtools view -bS "+bugName+" > "+inputname+".bam"</span></td>
|
|
|
940 </tr>
|
|
|
941 <tr>
|
|
|
942 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
|
|
|
943 <td id="LC55" 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><span class="pl-k">+</span>quietString</td>
|
|
|
944 </tr>
|
|
|
945 <tr>
|
|
|
946 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
|
|
|
947 <td id="LC56" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(argString)</span></td>
|
|
|
948 </tr>
|
|
|
949 <tr>
|
|
|
950 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
|
|
|
951 <td id="LC57" 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>
|
|
|
952 </tr>
|
|
|
953 <tr>
|
|
|
954 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
|
|
|
955 <td id="LC58" class="blob-code blob-code-inner js-file-line">
|
|
|
956 </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">
|
|
|
961 </td>
|
|
|
962 </tr>
|
|
|
963 <tr>
|
|
|
964 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
|
|
|
965 <td id="LC60" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "samtools sort "+bugName+" -o "+inputname+".sorted"</span></td>
|
|
|
966 </tr>
|
|
|
967 <tr>
|
|
|
968 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
|
|
|
969 <td id="LC61" 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><span class="pl-k">+</span>quietString</td>
|
|
|
970 </tr>
|
|
|
971 <tr>
|
|
|
972 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
|
|
|
973 <td id="LC62" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("argstring = "+argString)</span></td>
|
|
|
974 </tr>
|
|
|
975 <tr>
|
|
|
976 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
|
|
|
977 <td id="LC63" 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>
|
|
|
978 </tr>
|
|
|
979 <tr>
|
|
|
980 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
|
|
|
981 <td id="LC64" class="blob-code blob-code-inner js-file-line">
|
|
|
982 </td>
|
|
|
983 </tr>
|
|
|
984 <tr>
|
|
|
985 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
|
|
|
986 <td id="LC65" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "samtools index "+bugName+".sorted "+inputname+".sorted.bai"</span></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"> 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><span class="pl-k">+</span>quietString</td>
|
|
|
991 </tr>
|
|
|
992 <tr>
|
|
|
993 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
|
|
|
994 <td id="LC67" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("argstring = " + argString)</span></td>
|
|
|
995 </tr>
|
|
|
996 <tr>
|
|
|
997 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
|
|
|
998 <td id="LC68" 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>
|
|
|
999 </tr>
|
|
|
1000 <tr>
|
|
|
1001 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
|
|
|
1002 <td id="LC69" class="blob-code blob-code-inner js-file-line">
|
|
|
1003 </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">
|
|
|
1008 </td>
|
|
|
1009 </tr>
|
|
|
1010 <tr>
|
|
|
1011 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
|
|
|
1012 <td id="LC71" class="blob-code blob-code-inner js-file-line">
|
|
|
1013 </td>
|
|
|
1014 </tr>
|
|
|
1015 <tr>
|
|
|
1016 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
|
|
|
1017 <td id="LC72" class="blob-code blob-code-inner js-file-line">
|
|
|
1018 </td>
|
|
|
1019 </tr>
|
|
|
1020 <tr>
|
|
|
1021 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
|
|
|
1022 <td id="LC73" 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>, <span class="pl-smi">strain</span>):</td>
|
|
|
1023 </tr>
|
|
|
1024 <tr>
|
|
|
1025 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
|
|
|
1026 <td id="LC74" 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>
|
|
|
1027 </tr>
|
|
|
1028 <tr>
|
|
|
1029 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
|
|
|
1030 <td id="LC75" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span> defasult</span></td>
|
|
|
1031 </tr>
|
|
|
1032 <tr>
|
|
|
1033 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
|
|
|
1034 <td id="LC76" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td>
|
|
|
1035 </tr>
|
|
|
1036 <tr>
|
|
|
1037 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
|
|
|
1038 <td id="LC77" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">"</span></span></td>
|
|
|
1039 </tr>
|
|
|
1040 <tr>
|
|
|
1041 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
|
|
|
1042 <td id="LC78" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td>
|
|
|
1043 </tr>
|
|
|
1044 <tr>
|
|
|
1045 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
|
|
|
1046 <td id="LC79" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/IL3000.gtf<span class="pl-pds">"</span></span></td>
|
|
|
1047 </tr>
|
|
|
1048 <tr>
|
|
|
1049 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
|
|
|
1050 <td id="LC80" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "cufflinks -G Reference/IL3000.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"</span></td>
|
|
|
1051 </tr>
|
|
|
1052 <tr>
|
|
|
1053 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
|
|
|
1054 <td id="LC81" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "cufflinks -G Reference/ORFAnnotation.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"</span></td>
|
|
|
1055 </tr>
|
|
|
1056 <tr>
|
|
|
1057 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
|
|
|
1058 <td id="LC82" 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 -q -G <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> -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><span class="pl-k">+</span>quietString</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"> 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>
|
|
|
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">
|
|
|
1067 </td>
|
|
|
1068 </tr>
|
|
|
1069 <tr>
|
|
|
1070 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
|
|
|
1071 <td id="LC85" class="blob-code blob-code-inner js-file-line">
|
|
|
1072 </td>
|
|
|
1073 </tr>
|
|
|
1074 <tr>
|
|
|
1075 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
|
|
|
1076 <td id="LC86" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">convertToFasta</span>(<span class="pl-smi">inputName</span>, <span class="pl-smi">strain</span>): <span class="pl-c"><span class="pl-c">#</span>equivalent to Sara's awk scripte</span></td>
|
|
|
1077 </tr>
|
|
|
1078 <tr>
|
|
|
1079 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
|
|
|
1080 <td id="LC87" 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>
|
|
|
1081 </tr>
|
|
|
1082 <tr>
|
|
|
1083 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
|
|
|
1084 <td id="LC88" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span> default</span></td>
|
|
|
1085 </tr>
|
|
|
1086 <tr>
|
|
|
1087 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
|
|
|
1088 <td id="LC89" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td>
|
|
|
1089 </tr>
|
|
|
1090 <tr>
|
|
|
1091 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
|
|
|
1092 <td id="LC90" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/148_prot.fasta<span class="pl-pds">"</span></span></td>
|
|
|
1093 </tr>
|
|
|
1094 <tr>
|
|
|
1095 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
|
|
|
1096 <td id="LC91" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td>
|
|
|
1097 </tr>
|
|
|
1098 <tr>
|
|
|
1099 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
|
|
|
1100 <td id="LC92" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/IL3000_prot.fasta<span class="pl-pds">"</span></span></td>
|
|
|
1101 </tr>
|
|
|
1102 <tr>
|
|
|
1103 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
|
|
|
1104 <td id="LC93" class="blob-code blob-code-inner js-file-line">
|
|
|
1105 </td>
|
|
|
1106 </tr>
|
|
|
1107 <tr>
|
|
|
1108 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
|
|
|
1109 <td id="LC94" class="blob-code blob-code-inner js-file-line"> cuff_df <span class="pl-k">=</span> pd.read_csv(inputName<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>
|
|
|
1110 </tr>
|
|
|
1111 <tr>
|
|
|
1112 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
|
|
|
1113 <td id="LC95" class="blob-code blob-code-inner js-file-line"> cuff_df <span class="pl-k">=</span> cuff_df[(cuff_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">0</span>)]</td>
|
|
|
1114 </tr>
|
|
|
1115 <tr>
|
|
|
1116 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
|
|
|
1117 <td id="LC96" class="blob-code blob-code-inner js-file-line"> cuff_df.to_csv(<span class="pl-s"><span class="pl-pds">"</span>cuffTest.csv<span class="pl-pds">"</span></span>)</td>
|
|
|
1118 </tr>
|
|
|
1119 <tr>
|
|
|
1120 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
|
|
|
1121 <td id="LC97" class="blob-code blob-code-inner js-file-line"> gene_id_List <span class="pl-k">=</span> cuff_df[<span class="pl-s"><span class="pl-pds">'</span>gene_id<span class="pl-pds">'</span></span>].tolist()</td>
|
|
|
1122 </tr>
|
|
|
1123 <tr>
|
|
|
1124 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
|
|
|
1125 <td id="LC98" class="blob-code blob-code-inner js-file-line">
|
|
|
1126 </td>
|
|
|
1127 </tr>
|
|
|
1128 <tr>
|
|
|
1129 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
|
|
|
1130 <td id="LC99" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(gene_id_List)</span></td>
|
|
|
1131 </tr>
|
|
|
1132 <tr>
|
|
|
1133 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
|
|
|
1134 <td id="LC100" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print ("Found from 8880="+str(found))</span></td>
|
|
|
1135 </tr>
|
|
|
1136 <tr>
|
|
|
1137 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
|
|
|
1138 <td id="LC101" class="blob-code blob-code-inner js-file-line">
|
|
|
1139 </td>
|
|
|
1140 </tr>
|
|
|
1141 <tr>
|
|
|
1142 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
|
|
|
1143 <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> need to load in IL3000_prot.fasta</span></td>
|
|
|
1144 </tr>
|
|
|
1145 <tr>
|
|
|
1146 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
|
|
|
1147 <td id="LC103" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> for each line with >TcIL3000_1_1940</span></td>
|
|
|
1148 </tr>
|
|
|
1149 <tr>
|
|
|
1150 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
|
|
|
1151 <td id="LC104" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> search within cuff_df[gene_id] for match</span></td>
|
|
|
1152 </tr>
|
|
|
1153 <tr>
|
|
|
1154 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
|
|
|
1155 <td id="LC105" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> add it to the outfile. (need to save it as used by hmmer later</span></td>
|
|
|
1156 </tr>
|
|
|
1157 <tr>
|
|
|
1158 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
|
|
|
1159 <td id="LC106" class="blob-code blob-code-inner js-file-line"> number <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1160 </tr>
|
|
|
1161 <tr>
|
|
|
1162 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
|
|
|
1163 <td id="LC107" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">all</span> <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1164 </tr>
|
|
|
1165 <tr>
|
|
|
1166 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
|
|
|
1167 <td id="LC108" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(inputName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_6frame.fas<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>
|
|
|
1168 </tr>
|
|
|
1169 <tr>
|
|
|
1170 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
|
|
|
1171 <td id="LC109" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> <span class="pl-c1">open</span>(refName,<span class="pl-s"><span class="pl-pds">'</span>r<span class="pl-pds">'</span></span>)</td>
|
|
|
1172 </tr>
|
|
|
1173 <tr>
|
|
|
1174 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
|
|
|
1175 <td id="LC110" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ref = open(r"Reference/IL3000_prot.fasta",'r')</span></td>
|
|
|
1176 </tr>
|
|
|
1177 <tr>
|
|
|
1178 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
|
|
|
1179 <td id="LC111" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1180 </tr>
|
|
|
1181 <tr>
|
|
|
1182 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
|
|
|
1183 <td id="LC112" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td>
|
|
|
1184 </tr>
|
|
|
1185 <tr>
|
|
|
1186 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
|
|
|
1187 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">while</span> line:</td>
|
|
|
1188 </tr>
|
|
|
1189 <tr>
|
|
|
1190 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
|
|
|
1191 <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line[<span class="pl-c1">0</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>:</td>
|
|
|
1192 </tr>
|
|
|
1193 <tr>
|
|
|
1194 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
|
|
|
1195 <td id="LC115" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">all</span> <span class="pl-k">=</span> <span class="pl-c1">all</span><span class="pl-k">+</span><span class="pl-c1">1</span></td>
|
|
|
1196 </tr>
|
|
|
1197 <tr>
|
|
|
1198 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
|
|
|
1199 <td id="LC116" class="blob-code blob-code-inner js-file-line"> ln <span class="pl-k">=</span> line[<span class="pl-c1">1</span>:] <span class="pl-c"><span class="pl-c">#</span>remove ></span></td>
|
|
|
1200 </tr>
|
|
|
1201 <tr>
|
|
|
1202 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
|
|
|
1203 <td id="LC117" class="blob-code blob-code-inner js-file-line"> ln <span class="pl-k">=</span> ln.rstrip() <span class="pl-c"><span class="pl-c">#</span>remove /n /r etc</span></td>
|
|
|
1204 </tr>
|
|
|
1205 <tr>
|
|
|
1206 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
|
|
|
1207 <td id="LC118" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (ln)</span></td>
|
|
|
1208 </tr>
|
|
|
1209 <tr>
|
|
|
1210 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
|
|
|
1211 <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> ln <span class="pl-k">in</span> gene_id_List:</td>
|
|
|
1212 </tr>
|
|
|
1213 <tr>
|
|
|
1214 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
|
|
|
1215 <td id="LC120" class="blob-code blob-code-inner js-file-line"> number <span class="pl-k">=</span> number<span class="pl-k">+</span><span class="pl-c1">1</span></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"> outfile.write(line)</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"> line <span class="pl-k">=</span> ref.readline()</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"> <span class="pl-k">if</span> line:</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-k">while</span> line[<span class="pl-c1">0</span>] <span class="pl-k">!=</span> <span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>:</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"> outfile.write(line)</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"> line<span class="pl-k">=</span>ref.readline()</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">if</span> <span class="pl-k">not</span> line:</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"> <span class="pl-k">break</span><span class="pl-bu">;</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"> <span class="pl-k">else</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"> line <span class="pl-k">=</span> ref.readline()</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"> <span class="pl-k">else</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"> line <span class="pl-k">=</span>ref.readline()</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"> ref.close()</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"> <span class="pl-c1">print</span>(<span class="pl-c1">str</span>(<span class="pl-c1">len</span>(gene_id_List))<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><span class="pl-c1">str</span>(number)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> from <span class="pl-pds">"</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(<span class="pl-c1">all</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"> <span class="pl-k">return</span> cuff_df</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">
|
|
|
1280 </td>
|
|
|
1281 </tr>
|
|
|
1282 <tr>
|
|
|
1283 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
|
|
|
1284 <td id="LC137" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">HMMerMotifSearch</span>(<span class="pl-smi">name</span>, <span class="pl-smi">strain</span>, <span class="pl-smi">cuff_df</span>):</td>
|
|
|
1285 </tr>
|
|
|
1286 <tr>
|
|
|
1287 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
|
|
|
1288 <td id="LC138" class="blob-code blob-code-inner js-file-line"> motifs <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>1<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>2a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>2b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>3<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>4a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>4b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>4c<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>5<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>6<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>7<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>8a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>8b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>9a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>9b<span class="pl-pds">'</span></span>,</td>
|
|
|
1289 </tr>
|
|
|
1290 <tr>
|
|
|
1291 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
|
|
|
1292 <td id="LC139" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>9c<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>10a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>10b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>11a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>11b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>12<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>13a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>13b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>13c<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>13d<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>14<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>15a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>15b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>15c<span class="pl-pds">'</span></span>]</td>
|
|
|
1293 </tr>
|
|
|
1294 <tr>
|
|
|
1295 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
|
|
|
1296 <td id="LC140" 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>
|
|
|
1297 </tr>
|
|
|
1298 <tr>
|
|
|
1299 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
|
|
|
1300 <td id="LC141" class="blob-code blob-code-inner js-file-line"> phylopath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Motifs/Phylotype<span class="pl-pds">"</span></span></td>
|
|
|
1301 </tr>
|
|
|
1302 <tr>
|
|
|
1303 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
|
|
|
1304 <td id="LC142" class="blob-code blob-code-inner js-file-line"> lineCounts <span class="pl-k">=</span> []</td>
|
|
|
1305 </tr>
|
|
|
1306 <tr>
|
|
|
1307 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
|
|
|
1308 <td id="LC143" class="blob-code blob-code-inner js-file-line"> compoundList <span class="pl-k">=</span> []</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"> <span class="pl-k">for</span> m <span class="pl-k">in</span> motifs:</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"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>hmmsearch <span class="pl-pds">"</span></span><span class="pl-k">+</span>phylopath <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.hmm <span class="pl-pds">"</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_6frame.fas > Phy<span class="pl-pds">"</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.out<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-c1">print</span>(argString)</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"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1325 </tr>
|
|
|
1326 <tr>
|
|
|
1327 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
|
|
|
1328 <td id="LC148" class="blob-code blob-code-inner js-file-line"> hmmResult <span class="pl-k">=</span> <span class="pl-c1">open</span>(<span class="pl-s"><span class="pl-pds">"</span>Phy<span class="pl-pds">"</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.out<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">'</span>r<span class="pl-pds">'</span></span>)</td>
|
|
|
1329 </tr>
|
|
|
1330 <tr>
|
|
|
1331 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
|
|
|
1332 <td id="LC149" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Tc148[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,8}</span><span class="pl-pds">"</span></span></td>
|
|
|
1333 </tr>
|
|
|
1334 <tr>
|
|
|
1335 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
|
|
|
1336 <td id="LC150" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td>
|
|
|
1337 </tr>
|
|
|
1338 <tr>
|
|
|
1339 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
|
|
|
1340 <td id="LC151" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Tc148[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,8}</span><span class="pl-pds">"</span></span></td>
|
|
|
1341 </tr>
|
|
|
1342 <tr>
|
|
|
1343 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
|
|
|
1344 <td id="LC152" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td>
|
|
|
1345 </tr>
|
|
|
1346 <tr>
|
|
|
1347 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
|
|
|
1348 <td id="LC153" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>TcIL3000_[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,4}</span>_[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,5}</span><span class="pl-pds">"</span></span></td>
|
|
|
1349 </tr>
|
|
|
1350 <tr>
|
|
|
1351 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
|
|
|
1352 <td id="LC154" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1353 </tr>
|
|
|
1354 <tr>
|
|
|
1355 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
|
|
|
1356 <td id="LC155" class="blob-code blob-code-inner js-file-line"> outList <span class="pl-k">=</span> []</td>
|
|
|
1357 </tr>
|
|
|
1358 <tr>
|
|
|
1359 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
|
|
|
1360 <td id="LC156" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> line <span class="pl-k">in</span> hmmResult:</td>
|
|
|
1361 </tr>
|
|
|
1362 <tr>
|
|
|
1363 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
|
|
|
1364 <td id="LC157" class="blob-code blob-code-inner js-file-line"> m <span class="pl-k">=</span> re.search(regex, line)</td>
|
|
|
1365 </tr>
|
|
|
1366 <tr>
|
|
|
1367 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
|
|
|
1368 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> m:</td>
|
|
|
1369 </tr>
|
|
|
1370 <tr>
|
|
|
1371 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
|
|
|
1372 <td id="LC159" class="blob-code blob-code-inner js-file-line"> outList.append(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>m.group())</td>
|
|
|
1373 </tr>
|
|
|
1374 <tr>
|
|
|
1375 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
|
|
|
1376 <td id="LC160" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">+=</span> <span class="pl-c1">1</span></td>
|
|
|
1377 </tr>
|
|
|
1378 <tr>
|
|
|
1379 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
|
|
|
1380 <td id="LC161" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> re.search(<span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>inclusion<span class="pl-pds">"</span></span>, line):</td>
|
|
|
1381 </tr>
|
|
|
1382 <tr>
|
|
|
1383 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
|
|
|
1384 <td id="LC162" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>inclusion threshold reached<span class="pl-pds">"</span></span>)</td>
|
|
|
1385 </tr>
|
|
|
1386 <tr>
|
|
|
1387 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
|
|
|
1388 <td id="LC163" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span></td>
|
|
|
1389 </tr>
|
|
|
1390 <tr>
|
|
|
1391 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
|
|
|
1392 <td id="LC164" class="blob-code blob-code-inner js-file-line"> compoundList.append(outList)</td>
|
|
|
1393 </tr>
|
|
|
1394 <tr>
|
|
|
1395 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
|
|
|
1396 <td id="LC165" class="blob-code blob-code-inner js-file-line"> lineCounts.append(n)</td>
|
|
|
1397 </tr>
|
|
|
1398 <tr>
|
|
|
1399 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
|
|
|
1400 <td id="LC166" class="blob-code blob-code-inner js-file-line"> hmmResult.close()</td>
|
|
|
1401 </tr>
|
|
|
1402 <tr>
|
|
|
1403 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
|
|
|
1404 <td id="LC167" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(lineCounts)</span></td>
|
|
|
1405 </tr>
|
|
|
1406 <tr>
|
|
|
1407 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
|
|
|
1408 <td id="LC168" class="blob-code blob-code-inner js-file-line">
|
|
|
1409 </td>
|
|
|
1410 </tr>
|
|
|
1411 <tr>
|
|
|
1412 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
|
|
|
1413 <td id="LC169" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(cuff_df)</span></td>
|
|
|
1414 </tr>
|
|
|
1415 <tr>
|
|
|
1416 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
|
|
|
1417 <td id="LC170" class="blob-code blob-code-inner js-file-line"> concatGroups <span class="pl-k">=</span> [<span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">3</span>, <span class="pl-c1">2</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">4</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>]</td>
|
|
|
1418 </tr>
|
|
|
1419 <tr>
|
|
|
1420 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
|
|
|
1421 <td id="LC171" class="blob-code blob-code-inner js-file-line"> countList <span class="pl-k">=</span> []</td>
|
|
|
1422 </tr>
|
|
|
1423 <tr>
|
|
|
1424 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
|
|
|
1425 <td id="LC172" class="blob-code blob-code-inner js-file-line"> weightList <span class="pl-k">=</span> []</td>
|
|
|
1426 </tr>
|
|
|
1427 <tr>
|
|
|
1428 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
|
|
|
1429 <td id="LC173" class="blob-code blob-code-inner js-file-line"> countIndex <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1430 </tr>
|
|
|
1431 <tr>
|
|
|
1432 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
|
|
|
1433 <td id="LC174" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1434 </tr>
|
|
|
1435 <tr>
|
|
|
1436 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
|
|
|
1437 <td id="LC175" class="blob-code blob-code-inner js-file-line"> totalWeigth <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1438 </tr>
|
|
|
1439 <tr>
|
|
|
1440 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
|
|
|
1441 <td id="LC176" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> c <span class="pl-k">in</span> concatGroups:</td>
|
|
|
1442 </tr>
|
|
|
1443 <tr>
|
|
|
1444 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
|
|
|
1445 <td id="LC177" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> []</td>
|
|
|
1446 </tr>
|
|
|
1447 <tr>
|
|
|
1448 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
|
|
|
1449 <td id="LC178" class="blob-code blob-code-inner js-file-line"> weight <span class="pl-k">=</span> []</td>
|
|
|
1450 </tr>
|
|
|
1451 <tr>
|
|
|
1452 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
|
|
|
1453 <td id="LC179" 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>, c):</td>
|
|
|
1454 </tr>
|
|
|
1455 <tr>
|
|
|
1456 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
|
|
|
1457 <td id="LC180" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> a <span class="pl-k">+</span> compoundList.pop(<span class="pl-c1">0</span>)</td>
|
|
|
1458 </tr>
|
|
|
1459 <tr>
|
|
|
1460 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
|
|
|
1461 <td id="LC181" class="blob-code blob-code-inner js-file-line"> t <span class="pl-k">=</span> <span class="pl-c1">set</span>(a)</td>
|
|
|
1462 </tr>
|
|
|
1463 <tr>
|
|
|
1464 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
|
|
|
1465 <td id="LC182" class="blob-code blob-code-inner js-file-line"> countList.append(<span class="pl-c1">len</span>(t))</td>
|
|
|
1466 </tr>
|
|
|
1467 <tr>
|
|
|
1468 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
|
|
|
1469 <td id="LC183" class="blob-code blob-code-inner js-file-line"> wa <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1470 </tr>
|
|
|
1471 <tr>
|
|
|
1472 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
|
|
|
1473 <td id="LC184" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> w <span class="pl-k">in</span> t:</td>
|
|
|
1474 </tr>
|
|
|
1475 <tr>
|
|
|
1476 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
|
|
|
1477 <td id="LC185" class="blob-code blob-code-inner js-file-line"> wt <span class="pl-k">=</span> cuff_df.loc[cuff_df[<span class="pl-s"><span class="pl-pds">'</span>gene_id<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> w, <span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].iloc[<span class="pl-c1">0</span>]</td>
|
|
|
1478 </tr>
|
|
|
1479 <tr>
|
|
|
1480 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
|
|
|
1481 <td id="LC186" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(w)</span></td>
|
|
|
1482 </tr>
|
|
|
1483 <tr>
|
|
|
1484 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
|
|
|
1485 <td id="LC187" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(wt)</span></td>
|
|
|
1486 </tr>
|
|
|
1487 <tr>
|
|
|
1488 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
|
|
|
1489 <td id="LC188" class="blob-code blob-code-inner js-file-line"> wa <span class="pl-k">=</span> wa<span class="pl-k">+</span>wt</td>
|
|
|
1490 </tr>
|
|
|
1491 <tr>
|
|
|
1492 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
|
|
|
1493 <td id="LC189" class="blob-code blob-code-inner js-file-line"> weightList.append(wa)</td>
|
|
|
1494 </tr>
|
|
|
1495 <tr>
|
|
|
1496 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
|
|
|
1497 <td id="LC190" class="blob-code blob-code-inner js-file-line"> totalWeigth<span class="pl-k">+=</span>wa</td>
|
|
|
1498 </tr>
|
|
|
1499 <tr>
|
|
|
1500 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
|
|
|
1501 <td id="LC191" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">+=</span> <span class="pl-c1">len</span>(t)</td>
|
|
|
1502 </tr>
|
|
|
1503 <tr>
|
|
|
1504 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
|
|
|
1505 <td id="LC192" class="blob-code blob-code-inner js-file-line"> countList.append(totalCount)</td>
|
|
|
1506 </tr>
|
|
|
1507 <tr>
|
|
|
1508 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
|
|
|
1509 <td id="LC193" class="blob-code blob-code-inner js-file-line"> weightList.append(totalWeigth)</td>
|
|
|
1510 </tr>
|
|
|
1511 <tr>
|
|
|
1512 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
|
|
|
1513 <td id="LC194" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(countList)</span></td>
|
|
|
1514 </tr>
|
|
|
1515 <tr>
|
|
|
1516 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
|
|
|
1517 <td id="LC195" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("--------")</span></td>
|
|
|
1518 </tr>
|
|
|
1519 <tr>
|
|
|
1520 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
|
|
|
1521 <td id="LC196" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(weightList)</span></td>
|
|
|
1522 </tr>
|
|
|
1523 <tr>
|
|
|
1524 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
|
|
|
1525 <td id="LC197" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("--------")</span></td>
|
|
|
1526 </tr>
|
|
|
1527 <tr>
|
|
|
1528 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
|
|
|
1529 <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> countList,weightList</td>
|
|
|
1530 </tr>
|
|
|
1531 <tr>
|
|
|
1532 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
|
|
|
1533 <td id="LC199" class="blob-code blob-code-inner js-file-line">
|
|
|
1534 </td>
|
|
|
1535 </tr>
|
|
|
1536 <tr>
|
|
|
1537 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
|
|
|
1538 <td id="LC200" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">relativeFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td>
|
|
|
1539 </tr>
|
|
|
1540 <tr>
|
|
|
1541 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
|
|
|
1542 <td id="LC201" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td>
|
|
|
1543 </tr>
|
|
|
1544 <tr>
|
|
|
1545 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
|
|
|
1546 <td id="LC202" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</span>])</td>
|
|
|
1547 </tr>
|
|
|
1548 <tr>
|
|
|
1549 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
|
|
|
1550 <td id="LC203" 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">15</span>):</td>
|
|
|
1551 </tr>
|
|
|
1552 <tr>
|
|
|
1553 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
|
|
|
1554 <td id="LC204" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td>
|
|
|
1555 </tr>
|
|
|
1556 <tr>
|
|
|
1557 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
|
|
|
1558 <td id="LC205" class="blob-code blob-code-inner js-file-line">
|
|
|
1559 </td>
|
|
|
1560 </tr>
|
|
|
1561 <tr>
|
|
|
1562 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
|
|
|
1563 <td id="LC206" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>: pList, <span class="pl-s"><span class="pl-pds">'</span>Relative Frequency<span class="pl-pds">'</span></span>: relFreqList}</td>
|
|
|
1564 </tr>
|
|
|
1565 <tr>
|
|
|
1566 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
|
|
|
1567 <td id="LC207" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td>
|
|
|
1568 </tr>
|
|
|
1569 <tr>
|
|
|
1570 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
|
|
|
1571 <td id="LC208" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> htmlresource<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> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_t_relative_frequency.csv<span class="pl-pds">"</span></span></td>
|
|
|
1572 </tr>
|
|
|
1573 <tr>
|
|
|
1574 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
|
|
|
1575 <td id="LC209" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td>
|
|
|
1576 </tr>
|
|
|
1577 <tr>
|
|
|
1578 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
|
|
|
1579 <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> relFreqList <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></td>
|
|
|
1580 </tr>
|
|
|
1581 <tr>
|
|
|
1582 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
|
|
|
1583 <td id="LC211" class="blob-code blob-code-inner js-file-line">
|
|
|
1584 </td>
|
|
|
1585 </tr>
|
|
|
1586 <tr>
|
|
|
1587 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
|
|
|
1588 <td id="LC212" class="blob-code blob-code-inner js-file-line">
|
|
|
1589 </td>
|
|
|
1590 </tr>
|
|
|
1591 <tr>
|
|
|
1592 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
|
|
|
1593 <td id="LC213" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">weightedFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td>
|
|
|
1594 </tr>
|
|
|
1595 <tr>
|
|
|
1596 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
|
|
|
1597 <td id="LC214" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td>
|
|
|
1598 </tr>
|
|
|
1599 <tr>
|
|
|
1600 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
|
|
|
1601 <td id="LC215" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</span>])</td>
|
|
|
1602 </tr>
|
|
|
1603 <tr>
|
|
|
1604 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
|
|
|
1605 <td id="LC216" 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">15</span>):</td>
|
|
|
1606 </tr>
|
|
|
1607 <tr>
|
|
|
1608 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
|
|
|
1609 <td id="LC217" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td>
|
|
|
1610 </tr>
|
|
|
1611 <tr>
|
|
|
1612 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
|
|
|
1613 <td id="LC218" class="blob-code blob-code-inner js-file-line">
|
|
|
1614 </td>
|
|
|
1615 </tr>
|
|
|
1616 <tr>
|
|
|
1617 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
|
|
|
1618 <td id="LC219" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>: pList, <span class="pl-s"><span class="pl-pds">'</span>Weighted Frequency<span class="pl-pds">'</span></span>: relFreqList}</td>
|
|
|
1619 </tr>
|
|
|
1620 <tr>
|
|
|
1621 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
|
|
|
1622 <td id="LC220" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td>
|
|
|
1623 </tr>
|
|
|
1624 <tr>
|
|
|
1625 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
|
|
|
1626 <td id="LC221" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> htmlresource<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> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_t_weighted_frequency.csv<span class="pl-pds">"</span></span></td>
|
|
|
1627 </tr>
|
|
|
1628 <tr>
|
|
|
1629 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
|
|
|
1630 <td id="LC222" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td>
|
|
|
1631 </tr>
|
|
|
1632 <tr>
|
|
|
1633 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
|
|
|
1634 <td id="LC223" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> relFreqList <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></td>
|
|
|
1635 </tr>
|
|
|
1636 <tr>
|
|
|
1637 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
|
|
|
1638 <td id="LC224" class="blob-code blob-code-inner js-file-line">
|
|
|
1639 </td>
|
|
|
1640 </tr>
|
|
|
1641 <tr>
|
|
|
1642 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
|
|
|
1643 <td id="LC225" class="blob-code blob-code-inner js-file-line">
|
|
|
1644 </td>
|
|
|
1645 </tr>
|
|
|
1646 <tr>
|
|
|
1647 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
|
|
|
1648 <td id="LC226" class="blob-code blob-code-inner js-file-line">
|
|
|
1649 </td>
|
|
|
1650 </tr>
|
|
|
1651 <tr>
|
|
|
1652 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
|
|
|
1653 <td id="LC227" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createStackedBar</span>(<span class="pl-smi">name</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">strain</span>,<span class="pl-smi">pdf</span>,<span class="pl-smi">html_resource</span>):</td>
|
|
|
1654 </tr>
|
|
|
1655 <tr>
|
|
|
1656 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
|
|
|
1657 <td id="LC228" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">"</span>#0000ff<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#6495ed<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#00ffff<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#caff70<span class="pl-pds">"</span></span>,</td>
|
|
|
1658 </tr>
|
|
|
1659 <tr>
|
|
|
1660 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
|
|
|
1661 <td id="LC229" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>#228b22<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#528b8b<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#00ff00<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#a52a2a<span class="pl-pds">"</span></span>,</td>
|
|
|
1662 </tr>
|
|
|
1663 <tr>
|
|
|
1664 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
|
|
|
1665 <td id="LC230" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>#ff0000<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#ffff00<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#ffa500<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#ff1493<span class="pl-pds">"</span></span>,</td>
|
|
|
1666 </tr>
|
|
|
1667 <tr>
|
|
|
1668 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
|
|
|
1669 <td id="LC231" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>#9400d3<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#bebebe<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#000000<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#ff00ff<span class="pl-pds">"</span></span>]</td>
|
|
|
1670 </tr>
|
|
|
1671 <tr>
|
|
|
1672 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
|
|
|
1673 <td id="LC232" class="blob-code blob-code-inner js-file-line">
|
|
|
1674 </td>
|
|
|
1675 </tr>
|
|
|
1676 <tr>
|
|
|
1677 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
|
|
|
1678 <td id="LC233" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">VAP_148</span> <span class="pl-k">=</span> [<span class="pl-c1">0.072</span>, <span class="pl-c1">0.032</span>, <span class="pl-c1">0.032</span>, <span class="pl-c1">0.004</span>, <span class="pl-c1">0.007</span>,</td>
|
|
|
1679 </tr>
|
|
|
1680 <tr>
|
|
|
1681 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
|
|
|
1682 <td id="LC234" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.005</span>, <span class="pl-c1">0.202</span>, <span class="pl-c1">0.004</span>, <span class="pl-c1">0.006</span>, <span class="pl-c1">0.014</span>,</td>
|
|
|
1683 </tr>
|
|
|
1684 <tr>
|
|
|
1685 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
|
|
|
1686 <td id="LC235" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.130</span>, <span class="pl-c1">0.133</span>, <span class="pl-c1">0.054</span>, <span class="pl-c1">0.039</span>, <span class="pl-c1">0.265</span>]</td>
|
|
|
1687 </tr>
|
|
|
1688 <tr>
|
|
|
1689 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
|
|
|
1690 <td id="LC236" class="blob-code blob-code-inner js-file-line">
|
|
|
1691 </td>
|
|
|
1692 </tr>
|
|
|
1693 <tr>
|
|
|
1694 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
|
|
|
1695 <td id="LC237" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">VAP_IL3000</span> <span class="pl-k">=</span> [<span class="pl-c1">0.073</span>, <span class="pl-c1">0.040</span>, <span class="pl-c1">0.049</span>, <span class="pl-c1">0.018</span>, <span class="pl-c1">0.060</span>,</td>
|
|
|
1696 </tr>
|
|
|
1697 <tr>
|
|
|
1698 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
|
|
|
1699 <td id="LC238" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.055</span>, <span class="pl-c1">0.054</span>, <span class="pl-c1">0.025</span>, <span class="pl-c1">0.012</span>, <span class="pl-c1">0.060</span>,</td>
|
|
|
1700 </tr>
|
|
|
1701 <tr>
|
|
|
1702 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
|
|
|
1703 <td id="LC239" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.142</span>, <span class="pl-c1">0.100</span>, <span class="pl-c1">0.061</span>, <span class="pl-c1">0.078</span>, <span class="pl-c1">0.172</span>]</td>
|
|
|
1704 </tr>
|
|
|
1705 <tr>
|
|
|
1706 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
|
|
|
1707 <td id="LC240" 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>
|
|
|
1708 </tr>
|
|
|
1709 <tr>
|
|
|
1710 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
|
|
|
1711 <td id="LC241" 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>
|
|
|
1712 </tr>
|
|
|
1713 <tr>
|
|
|
1714 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
|
|
|
1715 <td id="LC242" class="blob-code blob-code-inner js-file-line">
|
|
|
1716 </td>
|
|
|
1717 </tr>
|
|
|
1718 <tr>
|
|
|
1719 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
|
|
|
1720 <td id="LC243" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td>
|
|
|
1721 </tr>
|
|
|
1722 <tr>
|
|
|
1723 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
|
|
|
1724 <td id="LC244" class="blob-code blob-code-inner js-file-line"> VAPtable <span class="pl-k">=</span> <span class="pl-c1">VAP_148</span></td>
|
|
|
1725 </tr>
|
|
|
1726 <tr>
|
|
|
1727 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
|
|
|
1728 <td id="LC245" class="blob-code blob-code-inner js-file-line"> VAPname<span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>Tc148<span class="pl-cce">\n</span>Genome VAP<span class="pl-pds">'</span></span></td>
|
|
|
1729 </tr>
|
|
|
1730 <tr>
|
|
|
1731 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
|
|
|
1732 <td id="LC246" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td>
|
|
|
1733 </tr>
|
|
|
1734 <tr>
|
|
|
1735 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
|
|
|
1736 <td id="LC247" class="blob-code blob-code-inner js-file-line"> VAPtable <span class="pl-k">=</span> <span class="pl-c1">VAP_IL3000</span></td>
|
|
|
1737 </tr>
|
|
|
1738 <tr>
|
|
|
1739 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
|
|
|
1740 <td id="LC248" class="blob-code blob-code-inner js-file-line"> VAPname<span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>IL3000<span class="pl-cce">\n</span>Genome VAP<span class="pl-pds">'</span></span></td>
|
|
|
1741 </tr>
|
|
|
1742 <tr>
|
|
|
1743 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
|
|
|
1744 <td id="LC249" class="blob-code blob-code-inner js-file-line"> width <span class="pl-k">=</span> <span class="pl-c1">0.35</span> <span class="pl-c"><span class="pl-c">#</span> the width of the bars: can also be len(x) sequence</span></td>
|
|
|
1745 </tr>
|
|
|
1746 <tr>
|
|
|
1747 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
|
|
|
1748 <td id="LC250" class="blob-code blob-code-inner js-file-line"> plots <span class="pl-k">=</span> []</td>
|
|
|
1749 </tr>
|
|
|
1750 <tr>
|
|
|
1751 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
|
|
|
1752 <td id="LC251" class="blob-code blob-code-inner js-file-line"> fpos <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1753 </tr>
|
|
|
1754 <tr>
|
|
|
1755 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
|
|
|
1756 <td id="LC252" class="blob-code blob-code-inner js-file-line"> vpos <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1757 </tr>
|
|
|
1758 <tr>
|
|
|
1759 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
|
|
|
1760 <td id="LC253" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td>
|
|
|
1761 </tr>
|
|
|
1762 <tr>
|
|
|
1763 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
|
|
|
1764 <td id="LC254" class="blob-code blob-code-inner js-file-line"> tp <span class="pl-k">=</span> plt.bar(<span class="pl-c1">0</span>, freqList[p], width, <span class="pl-v">color</span><span class="pl-k">=</span> palette[p], <span class="pl-v">bottom</span> <span class="pl-k">=</span> fpos)</td>
|
|
|
1765 </tr>
|
|
|
1766 <tr>
|
|
|
1767 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
|
|
|
1768 <td id="LC255" class="blob-code blob-code-inner js-file-line"> fpos <span class="pl-k">+=</span>freqList[p]</td>
|
|
|
1769 </tr>
|
|
|
1770 <tr>
|
|
|
1771 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
|
|
|
1772 <td id="LC256" class="blob-code blob-code-inner js-file-line">
|
|
|
1773 </td>
|
|
|
1774 </tr>
|
|
|
1775 <tr>
|
|
|
1776 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
|
|
|
1777 <td id="LC257" class="blob-code blob-code-inner js-file-line"> tp <span class="pl-k">=</span> plt.bar(<span class="pl-c1">1</span>, VAPtable[p], width, <span class="pl-v">color</span><span class="pl-k">=</span> palette[p], <span class="pl-v">bottom</span> <span class="pl-k">=</span> vpos)</td>
|
|
|
1778 </tr>
|
|
|
1779 <tr>
|
|
|
1780 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
|
|
|
1781 <td id="LC258" class="blob-code blob-code-inner js-file-line"> vpos <span class="pl-k">+=</span>VAPtable[p]</td>
|
|
|
1782 </tr>
|
|
|
1783 <tr>
|
|
|
1784 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
|
|
|
1785 <td id="LC259" class="blob-code blob-code-inner js-file-line">
|
|
|
1786 </td>
|
|
|
1787 </tr>
|
|
|
1788 <tr>
|
|
|
1789 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
|
|
|
1790 <td id="LC260" class="blob-code blob-code-inner js-file-line"> plots.append(tp)</td>
|
|
|
1791 </tr>
|
|
|
1792 <tr>
|
|
|
1793 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
|
|
|
1794 <td id="LC261" class="blob-code blob-code-inner js-file-line"> plt.xticks([<span class="pl-c1">0</span>,<span class="pl-c1">1</span>],[name,VAPname])</td>
|
|
|
1795 </tr>
|
|
|
1796 <tr>
|
|
|
1797 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
|
|
|
1798 <td id="LC262" class="blob-code blob-code-inner js-file-line"> plt.legend(plots[::<span class="pl-k">-</span><span class="pl-c1">1</span>],[<span class="pl-s"><span class="pl-pds">'</span>p15<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p14<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p13<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p12<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p11<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p10<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p9<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p8<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p7<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p6<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p5<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p4<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p3<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p2<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p1<span class="pl-pds">'</span></span>])</td>
|
|
|
1799 </tr>
|
|
|
1800 <tr>
|
|
|
1801 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
|
|
|
1802 <td id="LC263" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Figure Legend: The transcriptomic Variant Antigen Profile of $\itTrypanosoma$ $\itcongolense$ estimated as phylotype <span class="pl-pds">"</span></span> \</td>
|
|
|
1803 </tr>
|
|
|
1804 <tr>
|
|
|
1805 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
|
|
|
1806 <td id="LC264" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>proportion adjusted for transcript abundance and the reference genomic Variant Antigen Profile. <span class="pl-pds">"</span></span> \</td>
|
|
|
1807 </tr>
|
|
|
1808 <tr>
|
|
|
1809 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
|
|
|
1810 <td id="LC265" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>Data was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td>
|
|
|
1811 </tr>
|
|
|
1812 <tr>
|
|
|
1813 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
|
|
|
1814 <td id="LC266" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.title(title, wrap="True")</span></td>
|
|
|
1815 </tr>
|
|
|
1816 <tr>
|
|
|
1817 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
|
|
|
1818 <td id="LC267" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.text(-0.2, -0.05, title, va="top", transform=ax.transAxes, wrap="True")</span></td>
|
|
|
1819 </tr>
|
|
|
1820 <tr>
|
|
|
1821 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
|
|
|
1822 <td id="LC268" class="blob-code blob-code-inner js-file-line"> plt.text(<span class="pl-k">-</span><span class="pl-c1">0.3</span>, <span class="pl-k">-</span><span class="pl-c1">0.15</span>, title, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>top<span class="pl-pds">"</span></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>)</td>
|
|
|
1823 </tr>
|
|
|
1824 <tr>
|
|
|
1825 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
|
|
|
1826 <td id="LC269" class="blob-code blob-code-inner js-file-line"> plt.tight_layout(<span class="pl-v">pad</span><span class="pl-k">=</span><span class="pl-c1">1.5</span>)</td>
|
|
|
1827 </tr>
|
|
|
1828 <tr>
|
|
|
1829 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
|
|
|
1830 <td id="LC270" 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">0.3</span>,<span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.99</span>,<span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.125</span>,<span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>,<span class="pl-v">hspace</span><span class="pl-k">=</span><span class="pl-c1">0.2</span>,<span class="pl-v">wspace</span><span class="pl-k">=</span><span class="pl-c1">0.2</span>)</td>
|
|
|
1831 </tr>
|
|
|
1832 <tr>
|
|
|
1833 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
|
|
|
1834 <td id="LC271" class="blob-code blob-code-inner js-file-line">
|
|
|
1835 </td>
|
|
|
1836 </tr>
|
|
|
1837 <tr>
|
|
|
1838 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
|
|
|
1839 <td id="LC272" class="blob-code blob-code-inner js-file-line"> plt.savefig(html_resource <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/stackedbar.png<span class="pl-pds">"</span></span>)</td>
|
|
|
1840 </tr>
|
|
|
1841 <tr>
|
|
|
1842 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
|
|
|
1843 <td id="LC273" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> pdf <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td>
|
|
|
1844 </tr>
|
|
|
1845 <tr>
|
|
|
1846 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
|
|
|
1847 <td id="LC274" class="blob-code blob-code-inner js-file-line"> plt.savefig(html_resource <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/stackedbar.pdf<span class="pl-pds">"</span></span>)</td>
|
|
|
1848 </tr>
|
|
|
1849 <tr>
|
|
|
1850 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
|
|
|
1851 <td id="LC275" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
|
|
|
1852 </tr>
|
|
|
1853 <tr>
|
|
|
1854 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
|
|
|
1855 <td id="LC276" class="blob-code blob-code-inner js-file-line">
|
|
|
1856 </td>
|
|
|
1857 </tr>
|
|
|
1858 <tr>
|
|
|
1859 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
|
|
|
1860 <td id="LC277" class="blob-code blob-code-inner js-file-line">
|
|
|
1861 </td>
|
|
|
1862 </tr>
|
|
|
1863 <tr>
|
|
|
1864 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
|
|
|
1865 <td id="LC278" 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">name</span>,<span class="pl-smi">htmlfn</span>,<span class="pl-smi">htmlresource</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">weightList</span>):</td>
|
|
|
1866 </tr>
|
|
|
1867 <tr>
|
|
|
1868 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
|
|
|
1869 <td id="LC279" 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>
|
|
|
1870 </tr>
|
|
|
1871 <tr>
|
|
|
1872 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
|
|
|
1873 <td id="LC280" 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>congolense VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma congolense</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td>
|
|
|
1874 </tr>
|
|
|
1875 <tr>
|
|
|
1876 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
|
|
|
1877 <td id="LC281" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> name</td>
|
|
|
1878 </tr>
|
|
|
1879 <tr>
|
|
|
1880 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
|
|
|
1881 <td id="LC282" 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>
|
|
|
1882 </tr>
|
|
|
1883 <tr>
|
|
|
1884 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
|
|
|
1885 <td id="LC283" 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%'>Table Legend: Variant Antigen Profiles of a transcriptome of <i>Trypanosoma congolense</i> estimated as phylotype proportion. <span class="pl-pds">"</span></span> \</td>
|
|
|
1886 </tr>
|
|
|
1887 <tr>
|
|
|
1888 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
|
|
|
1889 <td id="LC284" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted frequency refers to the phylotype proportion based transcript abundance. <span class="pl-pds">"</span></span> \</td>
|
|
|
1890 </tr>
|
|
|
1891 <tr>
|
|
|
1892 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
|
|
|
1893 <td id="LC285" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td>
|
|
|
1894 </tr>
|
|
|
1895 <tr>
|
|
|
1896 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
|
|
|
1897 <td id="LC286" 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>
|
|
|
1898 </tr>
|
|
|
1899 <tr>
|
|
|
1900 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
|
|
|
1901 <td id="LC287" class="blob-code blob-code-inner js-file-line">
|
|
|
1902 </td>
|
|
|
1903 </tr>
|
|
|
1904 <tr>
|
|
|
1905 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
|
|
|
1906 <td id="LC288" 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%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><th>Relative Frequency</th><th>Weighted Frequency</th></tr><span class="pl-pds">"</span></span></td>
|
|
|
1907 </tr>
|
|
|
1908 <tr>
|
|
|
1909 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
|
|
|
1910 <td id="LC289" 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>
|
|
|
1911 </tr>
|
|
|
1912 <tr>
|
|
|
1913 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
|
|
|
1914 <td id="LC290" 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>
|
|
|
1915 </tr>
|
|
|
1916 <tr>
|
|
|
1917 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
|
|
|
1918 <td id="LC291" 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">15</span>):</td>
|
|
|
1919 </tr>
|
|
|
1920 <tr>
|
|
|
1921 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
|
|
|
1922 <td id="LC292" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(freqList[i], <span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td>
|
|
|
1923 </tr>
|
|
|
1924 <tr>
|
|
|
1925 <td id="L293" class="blob-num js-line-number" data-line-number="293"></td>
|
|
|
1926 <td id="LC293" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">format</span>(weightList[i], <span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td>
|
|
|
1927 </tr>
|
|
|
1928 <tr>
|
|
|
1929 <td id="L294" class="blob-num js-line-number" data-line-number="294"></td>
|
|
|
1930 <td id="LC294" 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>phy<span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(i <span class="pl-k">+</span> <span class="pl-c1">1</span>) <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> 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> w <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td></tr><span class="pl-pds">"</span></span></td>
|
|
|
1931 </tr>
|
|
|
1932 <tr>
|
|
|
1933 <td id="L295" class="blob-num js-line-number" data-line-number="295"></td>
|
|
|
1934 <td id="LC295" 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>
|
|
|
1935 </tr>
|
|
|
1936 <tr>
|
|
|
1937 <td id="L296" class="blob-num js-line-number" data-line-number="296"></td>
|
|
|
1938 <td id="LC296" 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><p> <h3>Stacked Bar chart of Phylotype Frequency</h3> The 'weighted' relative frequency of each phylotype alongside the VAP of selected strain<span class="pl-c1">.</span></p><span class="pl-pds">"</span></span></td>
|
|
|
1939 </tr>
|
|
|
1940 <tr>
|
|
|
1941 <td id="L297" class="blob-num js-line-number" data-line-number="297"></td>
|
|
|
1942 <td id="LC297" 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 = 'stackedbar<span class="pl-c1">.</span>png' alt='Stacked bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td>
|
|
|
1943 </tr>
|
|
|
1944 <tr>
|
|
|
1945 <td id="L298" class="blob-num js-line-number" data-line-number="298"></td>
|
|
|
1946 <td id="LC298" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
|
|
|
1947 </tr>
|
|
|
1948 <tr>
|
|
|
1949 <td id="L299" class="blob-num js-line-number" data-line-number="299"></td>
|
|
|
1950 <td id="LC299" class="blob-code blob-code-inner js-file-line">
|
|
|
1951 </td>
|
|
|
1952 </tr>
|
|
|
1953 <tr>
|
|
|
1954 <td id="L300" class="blob-num js-line-number" data-line-number="300"></td>
|
|
|
1955 <td id="LC300" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += r"<p><h3>The Deviation Heat Map and Dendogram</h3>The phylotype variation expressed as the deviation from your sample mean compared to the model dataset</p>"</span></td>
|
|
|
1956 </tr>
|
|
|
1957 <tr>
|
|
|
1958 <td id="L301" class="blob-num js-line-number" data-line-number="301"></td>
|
|
|
1959 <td id="LC301" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> imgString = r"<img src = 'dheatmap.png' alt='Deviation Heatmap' style='max-width:100%'><br><br>"</span></td>
|
|
|
1960 </tr>
|
|
|
1961 <tr>
|
|
|
1962 <td id="L302" class="blob-num js-line-number" data-line-number="302"></td>
|
|
|
1963 <td id="LC302" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += imgString</span></td>
|
|
|
1964 </tr>
|
|
|
1965 <tr>
|
|
|
1966 <td id="L303" class="blob-num js-line-number" data-line-number="303"></td>
|
|
|
1967 <td id="LC303" class="blob-code blob-code-inner js-file-line">
|
|
|
1968 </td>
|
|
|
1969 </tr>
|
|
|
1970 <tr>
|
|
|
1971 <td id="L304" class="blob-num js-line-number" data-line-number="304"></td>
|
|
|
1972 <td id="LC304" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += r"<p><h3>The Variation PCA plot</h3>PCA analysis corresponding to absolute variation. Colour coded according to location</p>"</span></td>
|
|
|
1973 </tr>
|
|
|
1974 <tr>
|
|
|
1975 <td id="L305" class="blob-num js-line-number" data-line-number="305"></td>
|
|
|
1976 <td id="LC305" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> imgString = r"<img src = 'vapPCA.png' alt='PCA Analysis' style='max-width:100%'><br><br>"</span></td>
|
|
|
1977 </tr>
|
|
|
1978 <tr>
|
|
|
1979 <td id="L306" class="blob-num js-line-number" data-line-number="306"></td>
|
|
|
1980 <td id="LC306" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += imgString + r"</div></body></html>"</span></td>
|
|
|
1981 </tr>
|
|
|
1982 <tr>
|
|
|
1983 <td id="L307" class="blob-num js-line-number" data-line-number="307"></td>
|
|
|
1984 <td id="LC307" class="blob-code blob-code-inner js-file-line">
|
|
|
1985 </td>
|
|
|
1986 </tr>
|
|
|
1987 <tr>
|
|
|
1988 <td id="L308" class="blob-num js-line-number" data-line-number="308"></td>
|
|
|
1989 <td id="LC308" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(htmlfn, <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td>
|
|
|
1990 </tr>
|
|
|
1991 <tr>
|
|
|
1992 <td id="L309" class="blob-num js-line-number" data-line-number="309"></td>
|
|
|
1993 <td id="LC309" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
|
|
|
1994 </tr>
|
|
|
1995 <tr>
|
|
|
1996 <td id="L310" class="blob-num js-line-number" data-line-number="310"></td>
|
|
|
1997 <td id="LC310" class="blob-code blob-code-inner js-file-line">
|
|
|
1998 </td>
|
|
|
1999 </tr>
|
|
|
2000 <tr>
|
|
|
2001 <td id="L311" class="blob-num js-line-number" data-line-number="311"></td>
|
|
|
2002 <td id="LC311" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}</span></td>
|
|
|
2003 </tr>
|
|
|
2004 <tr>
|
|
|
2005 <td id="L312" class="blob-num js-line-number" data-line-number="312"></td>
|
|
|
2006 <td id="LC312" 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">dict</span>):</td>
|
|
|
2007 </tr>
|
|
|
2008 <tr>
|
|
|
2009 <td id="L313" class="blob-num js-line-number" data-line-number="313"></td>
|
|
|
2010 <td id="LC313" class="blob-code blob-code-inner js-file-line"> transcriptMapping(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>]], args[dict[<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>
|
|
|
2011 </tr>
|
|
|
2012 <tr>
|
|
|
2013 <td id="L314" class="blob-num js-line-number" data-line-number="314"></td>
|
|
|
2014 <td id="LC314" class="blob-code blob-code-inner js-file-line"> processSamFiles(args[dict[<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>
|
|
|
2015 </tr>
|
|
|
2016 <tr>
|
|
|
2017 <td id="L315" class="blob-num js-line-number" data-line-number="315"></td>
|
|
|
2018 <td id="LC315" class="blob-code blob-code-inner js-file-line"> transcriptAbundance(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -> ?.cuff/*.*</span></td>
|
|
|
2019 </tr>
|
|
|
2020 <tr>
|
|
|
2021 <td id="L316" class="blob-num js-line-number" data-line-number="316"></td>
|
|
|
2022 <td id="LC316" class="blob-code blob-code-inner js-file-line"> cuff_df <span class="pl-k">=</span> convertToFasta(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]])</td>
|
|
|
2023 </tr>
|
|
|
2024 <tr>
|
|
|
2025 <td id="L317" class="blob-num js-line-number" data-line-number="317"></td>
|
|
|
2026 <td id="LC317" class="blob-code blob-code-inner js-file-line"> countList, weightList <span class="pl-k">=</span> HMMerMotifSearch(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]], cuff_df)</td>
|
|
|
2027 </tr>
|
|
|
2028 <tr>
|
|
|
2029 <td id="L318" class="blob-num js-line-number" data-line-number="318"></td>
|
|
|
2030 <td id="LC318" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> relativeFrequencyTable(countList,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]])</td>
|
|
|
2031 </tr>
|
|
|
2032 <tr>
|
|
|
2033 <td id="L319" class="blob-num js-line-number" data-line-number="319"></td>
|
|
|
2034 <td id="LC319" class="blob-code blob-code-inner js-file-line"> relWeightList <span class="pl-k">=</span> weightedFrequencyTable(weightList,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]])</td>
|
|
|
2035 </tr>
|
|
|
2036 <tr>
|
|
|
2037 <td id="L320" class="blob-num js-line-number" data-line-number="320"></td>
|
|
|
2038 <td id="LC320" class="blob-code blob-code-inner js-file-line"> createStackedBar(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],relWeightList, args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]])</td>
|
|
|
2039 </tr>
|
|
|
2040 <tr>
|
|
|
2041 <td id="L321" class="blob-num js-line-number" data-line-number="321"></td>
|
|
|
2042 <td id="LC321" class="blob-code blob-code-inner js-file-line"> createHTML(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]], relFreqList, relWeightList)</td>
|
|
|
2043 </tr>
|
|
|
2044 <tr>
|
|
|
2045 <td id="L322" class="blob-num js-line-number" data-line-number="322"></td>
|
|
|
2046 <td id="LC322" class="blob-code blob-code-inner js-file-line">
|
|
|
2047 </td>
|
|
|
2048 </tr>
|
|
|
2049 <tr>
|
|
|
2050 <td id="L323" class="blob-num js-line-number" data-line-number="323"></td>
|
|
|
2051 <td id="LC323" 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>
|
|
|
2052 </tr>
|
|
|
2053 <tr>
|
|
|
2054 <td id="L324" class="blob-num js-line-number" data-line-number="324"></td>
|
|
|
2055 <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("Commencing Transcript Mapping")</span></td>
|
|
|
2056 </tr>
|
|
|
2057 <tr>
|
|
|
2058 <td id="L325" class="blob-num js-line-number" data-line-number="325"></td>
|
|
|
2059 <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>transcriptMapping("T_Test", "Transcripts.1","Transcripts.2")</span></td>
|
|
|
2060 </tr>
|
|
|
2061 <tr>
|
|
|
2062 <td id="L326" class="blob-num js-line-number" data-line-number="326"></td>
|
|
|
2063 <td id="LC326" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("Processimg Sam Files")</span></td>
|
|
|
2064 </tr>
|
|
|
2065 <tr>
|
|
|
2066 <td id="L327" class="blob-num js-line-number" data-line-number="327"></td>
|
|
|
2067 <td id="LC327" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>processSamFiles("T_Test")</span></td>
|
|
|
2068 </tr>
|
|
|
2069 <tr>
|
|
|
2070 <td id="L328" class="blob-num js-line-number" data-line-number="328"></td>
|
|
|
2071 <td id="LC328" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("Assessing Transcript Abundance")</span></td>
|
|
|
2072 </tr>
|
|
|
2073 <tr>
|
|
|
2074 <td id="L329" class="blob-num js-line-number" data-line-number="329"></td>
|
|
|
2075 <td id="LC329" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>transcriptAbundance("T_Test")</span></td>
|
|
|
2076 </tr>
|
|
|
2077 <tr>
|
|
|
2078 <td id="L330" class="blob-num js-line-number" data-line-number="330"></td>
|
|
|
2079 <td id="LC330" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print ("Converting to Fasta Subset")</span></td>
|
|
|
2080 </tr>
|
|
|
2081 <tr>
|
|
|
2082 <td id="L331" class="blob-num js-line-number" data-line-number="331"></td>
|
|
|
2083 <td id="LC331" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cuff_df = convertToFasta("T_Test")</span></td>
|
|
|
2084 </tr>
|
|
|
2085 <tr>
|
|
|
2086 <td id="L332" class="blob-num js-line-number" data-line-number="332"></td>
|
|
|
2087 <td id="LC332" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("Commencing HMMer search")</span></td>
|
|
|
2088 </tr>
|
|
|
2089 <tr>
|
|
|
2090 <td id="L333" class="blob-num js-line-number" data-line-number="333"></td>
|
|
|
2091 <td id="LC333" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>countList, weightList = HMMerMotifSearch("T_Test",cuff_df)</span></td>
|
|
|
2092 </tr>
|
|
|
2093 <tr>
|
|
|
2094 <td id="L334" class="blob-num js-line-number" data-line-number="334"></td>
|
|
|
2095 <td id="LC334" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>relativeFrequencyTable(countList,'T_Test')</span></td>
|
|
|
2096 </tr>
|
|
|
2097 <tr>
|
|
|
2098 <td id="L335" class="blob-num js-line-number" data-line-number="335"></td>
|
|
|
2099 <td id="LC335" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>weightedFrequencyTable(weightList,'T_Test')</span></td>
|
|
|
2100 </tr>
|
|
|
2101 <tr>
|
|
|
2102 <td id="L336" class="blob-num js-line-number" data-line-number="336"></td>
|
|
|
2103 <td id="LC336" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> [<span class="pl-c1">0.111842105</span>,<span class="pl-c1">0.059210526</span>,<span class="pl-c1">0.026315789</span>,<span class="pl-c1">0.013157895</span>,</td>
|
|
|
2104 </tr>
|
|
|
2105 <tr>
|
|
|
2106 <td id="L337" class="blob-num js-line-number" data-line-number="337"></td>
|
|
|
2107 <td id="LC337" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.006578947</span>,<span class="pl-c1">0.013157895</span>,<span class="pl-c1">0.032894737</span>,<span class="pl-c1">0.019736842</span>,</td>
|
|
|
2108 </tr>
|
|
|
2109 <tr>
|
|
|
2110 <td id="L338" class="blob-num js-line-number" data-line-number="338"></td>
|
|
|
2111 <td id="LC338" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.039473684</span>,<span class="pl-c1">0.046052632</span>,<span class="pl-c1">0.217105263</span>,<span class="pl-c1">0.065789474</span>,</td>
|
|
|
2112 </tr>
|
|
|
2113 <tr>
|
|
|
2114 <td id="L339" class="blob-num js-line-number" data-line-number="339"></td>
|
|
|
2115 <td id="LC339" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.151315789</span>,<span class="pl-c1">0.059210526</span>,<span class="pl-c1">0.138157895</span>]</td>
|
|
|
2116 </tr>
|
|
|
2117 <tr>
|
|
|
2118 <td id="L340" class="blob-num js-line-number" data-line-number="340"></td>
|
|
|
2119 <td id="LC340" class="blob-code blob-code-inner js-file-line">
|
|
|
2120 </td>
|
|
|
2121 </tr>
|
|
|
2122 <tr>
|
|
|
2123 <td id="L341" class="blob-num js-line-number" data-line-number="341"></td>
|
|
|
2124 <td id="LC341" class="blob-code blob-code-inner js-file-line"> relWeightList <span class="pl-k">=</span> [<span class="pl-c1">0.07532571</span>,<span class="pl-c1">0.05900545</span>,<span class="pl-c1">0.009601452</span>,<span class="pl-c1">0.042357532</span>,<span class="pl-c1">0.01236219</span>,<span class="pl-c1">0.001675663</span>,<span class="pl-c1">0.04109726</span>,</td>
|
|
|
2125 </tr>
|
|
|
2126 <tr>
|
|
|
2127 <td id="L342" class="blob-num js-line-number" data-line-number="342"></td>
|
|
|
2128 <td id="LC342" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.097464248</span>,<span class="pl-c1">0.057491666</span>,<span class="pl-c1">0.05826875</span>,<span class="pl-c1">0.279457473</span>,<span class="pl-c1">0.070004772</span>,<span class="pl-c1">0.065329007</span>,<span class="pl-c1">0.085361298</span>,<span class="pl-c1">0.045197529</span>]</td>
|
|
|
2129 </tr>
|
|
|
2130 <tr>
|
|
|
2131 <td id="L343" class="blob-num js-line-number" data-line-number="343"></td>
|
|
|
2132 <td id="LC343" class="blob-code blob-code-inner js-file-line">
|
|
|
2133 </td>
|
|
|
2134 </tr>
|
|
|
2135 <tr>
|
|
|
2136 <td id="L344" class="blob-num js-line-number" data-line-number="344"></td>
|
|
|
2137 <td id="LC344" class="blob-code blob-code-inner js-file-line"> createStackedBar(<span class="pl-s"><span class="pl-pds">'</span>T_Test<span class="pl-pds">'</span></span>,relWeightList, <span class="pl-s"><span class="pl-pds">'</span>Tc148<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>results<span class="pl-pds">'</span></span>)</td>
|
|
|
2138 </tr>
|
|
|
2139 <tr>
|
|
|
2140 <td id="L345" class="blob-num js-line-number" data-line-number="345"></td>
|
|
|
2141 <td id="LC345" class="blob-code blob-code-inner js-file-line"> createHTML(<span class="pl-s"><span class="pl-pds">"</span>t_test<span class="pl-pds">"</span></span>,<span class="pl-s"><span class="pl-pds">"</span>results/t_test.html<span class="pl-pds">"</span></span>,<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>,relFreqList,relWeightList)</td>
|
|
|
2142 </tr>
|
|
|
2143 </table>
|
|
|
2144
|
|
|
2145 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
|
|
|
2146 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar">
|
|
|
2147 <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>
|
|
|
2148 </summary>
|
|
|
2149 <details-menu>
|
|
|
2150 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
|
|
|
2151 <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>
|
|
|
2152 <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>
|
|
|
2153 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/johnheap/VAPPER-Galaxy/blame/a4e16d71fe985f389930c02f94354b87d3aabadb/Tryp_T.py">View git blame</a></li>
|
|
|
2154 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li>
|
|
|
2155 </ul>
|
|
|
2156 </details-menu>
|
|
|
2157 </details>
|
|
|
2158
|
|
|
2159 </div>
|
|
|
2160
|
|
|
2161 </div>
|
|
|
2162
|
|
|
2163
|
|
|
2164
|
|
|
2165 <details class="details-reset details-overlay details-overlay-dark">
|
|
|
2166 <summary data-hotkey="l" aria-label="Jump to line"></summary>
|
|
|
2167 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
|
|
|
2168 <!-- '"` --><!-- </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="✓" />
|
|
|
2169 <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>
|
|
|
2170 <button type="submit" class="btn" data-close-dialog>Go</button>
|
|
|
2171 </form> </details-dialog>
|
|
|
2172 </details>
|
|
|
2173
|
|
|
2174
|
|
|
2175
|
|
|
2176 </div>
|
|
|
2177 <div class="modal-backdrop js-touch-events"></div>
|
|
|
2178 </div>
|
|
|
2179
|
|
|
2180 </main>
|
|
|
2181 </div>
|
|
|
2182
|
|
|
2183
|
|
|
2184 </div>
|
|
|
2185
|
|
|
2186
|
|
|
2187 <div class="footer container-lg width-full p-responsive" role="contentinfo">
|
|
|
2188 <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 ">
|
|
|
2189 <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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2190 <li class="mr-3 mr-lg-0">© 2019 <span title="0.38259s from unicorn-7478f9985c-skxnd">GitHub</span>, Inc.</li>
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2191 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li>
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2192 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li>
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2193 <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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2194 <li class="mr-3 mr-lg-0"><a href="https://githubstatus.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
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2195 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
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2196 </ul>
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2197
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2198 <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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2199 <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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2200 </a>
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2201 <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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2202 <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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2203 <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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2204 <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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2205 <li class="mr-3 mr-lg-0"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
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2206 <li class="mr-3 mr-lg-0"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
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2207 <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>
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2208
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2209 </ul>
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2210 </div>
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2211 <div class="d-flex flex-justify-center pb-6">
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2212 <span class="f6 text-gray-light"></span>
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|
2213 </div>
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2214 </div>
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2215
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2216
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2217
|
|
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2218 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
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|
|
2219 <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>
|
|
|
2220 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
|
|
|
2221 <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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2222 </button>
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2223 You can’t perform that action at this time.
|
|
|
2224 </div>
|
|
|
2225
|
|
|
2226
|
|
|
2227 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
|
|
|
2228 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
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|
|
2229
|
|
|
2230 <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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2231
|
|
|
2232
|
|
|
2233
|
|
|
2234 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
|
|
|
2235 >
|
|
|
2236 <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>
|
|
|
2237 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
|
|
|
2238 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
|
|
|
2239 </div>
|
|
|
2240 <template id="site-details-dialog">
|
|
|
2241 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
|
|
|
2242 <summary role="button" aria-label="Close dialog"></summary>
|
|
|
2243 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
|
|
|
2244 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
|
|
|
2245 <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>
|
|
|
2246 </button>
|
|
|
2247 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
|
|
|
2248 </details-dialog>
|
|
|
2249 </details>
|
|
|
2250 </template>
|
|
|
2251
|
|
|
2252 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
|
|
|
2253 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
|
|
|
2254 </div>
|
|
|
2255 </div>
|
|
|
2256
|
|
|
2257 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
|
|
|
2258
|
|
|
2259 </body>
|
|
|
2260 </html>
|
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|
2261
|
