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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=9nFC/TA6FDAKMuNXw3enOJF6Z5i01AOdbn0jyVKtcamwMA8oxN0iwjwD6g/Gk0mUkRYceloKa1EiDDQCCe/w6g=="
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279 spellcheck="false"
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280 autocomplete="off"
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281 >
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282 <input type="hidden" class="js-site-search-type-field" name="type" >
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283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
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284
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|
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285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
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286
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287 <ul class="d-none js-jump-to-suggestions-template-container">
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288
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289
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290 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option">
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291 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
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292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
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293 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
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294 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
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295 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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296 </div>
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297
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298 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
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299
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|
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300 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
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|
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301 </div>
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302
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|
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303 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
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304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
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305 In this repository
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306 </span>
|
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307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
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308 All GitHub
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309 </span>
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310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
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311 </div>
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312
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|
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313 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
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314 Jump to
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315 <span class="d-inline-block ml-1 v-align-middle">↵</span>
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316 </div>
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317 </a>
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318 </li>
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319
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320 </ul>
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321
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322 <ul class="d-none js-jump-to-no-results-template-container">
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323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2">
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324 <span class="text-gray">No suggested jump to results</span>
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325 </li>
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326 </ul>
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327
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328 <ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container">
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|
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329
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|
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330
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331 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option">
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332 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
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333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
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334 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
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335 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
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336 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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337 </div>
|
|
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338
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|
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339 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
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|
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340
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|
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341 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
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|
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342 </div>
|
|
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343
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|
|
344 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
|
|
|
345 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
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|
|
346 In this repository
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347 </span>
|
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|
348 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
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349 All GitHub
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350 </span>
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351 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
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352 </div>
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353
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354 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
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355 Jump to
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356 <span class="d-inline-block ml-1 v-align-middle">↵</span>
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357 </div>
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358 </a>
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359 </li>
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360
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361
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362
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363 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option">
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|
|
364 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
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|
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365 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
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366 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
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367 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
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368 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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369 </div>
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370
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371 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
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372
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|
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373 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
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|
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374 </div>
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375
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|
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376 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
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377 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
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378 In this repository
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379 </span>
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380 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
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381 All GitHub
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382 </span>
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383 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
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384 </div>
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385
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386 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
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387 Jump to
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604 <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/prompt_dismissals/signup" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="✓" /><input type="hidden" name="_method" value="put" /><input type="hidden" name="authenticity_token" value="rUlVltDIRxFtmVLWOALSaTw3jYYQnAkgOZNaBXl4TyU548taK3+va3xk4HBc3npM+B/jMCQq7vMKkG2ORne9cQ==" />
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609 <p class="col-6 mx-auto">GitHub is home to over 36 million developers working together to host and review code, manage projects, and build software together.</p>
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610 <a class="btn btn-primary" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"files signup prompt","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"A689:5C3D:C6144:14D916:5CF5617A","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_G.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="93e6383cc468287e90a1abe17ee3e6216b82b1b7d4ae0b4a616d22c192163882" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up" href="/join?source=prompt-blob-show">Sign up</a>
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656 Find file
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659 Copy path
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660 </clipboard-copy>
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664
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668 Fetching contributors…
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689 </div>
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709 </button>
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710 </div>
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711 </div>
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712 </div>
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713
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714
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715
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716 <div itemprop="text" class="Box-body p-0 blob-wrapper data type-python ">
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717
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718 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
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719 <tr>
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720 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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721 <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">"""</span></span></td>
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722 </tr>
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723 <tr>
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724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td>
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726 </tr>
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727 <tr>
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728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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729 <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author: John Heap, Computational Biology Facility, UoL</span></td>
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730 </tr>
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731 <tr>
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732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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733 <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td>
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734 </tr>
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735 <tr>
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736 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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737 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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738 </tr>
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739 <tr>
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740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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741 <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the "License");</span></td>
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742 </tr>
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743 <tr>
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744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
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745 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td>
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746 </tr>
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747 <tr>
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748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
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749 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td>
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750 </tr>
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751 <tr>
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752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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753 <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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754 </tr>
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755 <tr>
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756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
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757 <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td>
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758 </tr>
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759 <tr>
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760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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762 </tr>
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763 <tr>
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764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
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765 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td>
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766 </tr>
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767 <tr>
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768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
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769 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td>
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770 </tr>
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771 <tr>
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772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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773 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td>
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774 </tr>
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775 <tr>
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776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
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777 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td>
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778 </tr>
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779 <tr>
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780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
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781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td>
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782 </tr>
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783 <tr>
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784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
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785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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786 </tr>
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787 <tr>
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788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
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789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td>
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790 </tr>
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791 <tr>
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792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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793 <td id="LC19" class="blob-code blob-code-inner js-file-line">
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794 </td>
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795 </tr>
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796 <tr>
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797 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
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798 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td>
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799 </tr>
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800 <tr>
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801 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
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802 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td>
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803 </tr>
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804 <tr>
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805 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
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806 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td>
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807 </tr>
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808 <tr>
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809 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
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810 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
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811 </tr>
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812 <tr>
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813 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
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814 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td>
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815 </tr>
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816 <tr>
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817 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
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818 <td id="LC25" 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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819 </tr>
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820 <tr>
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821 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
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822 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> numpy <span class="pl-k">as</span> np</td>
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|
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823 </tr>
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824 <tr>
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825 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
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826 <td id="LC27" 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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827 </tr>
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828 <tr>
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829 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
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830 <td id="LC28" 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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831 </tr>
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832 <tr>
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833 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
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834 <td id="LC29" 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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835 </tr>
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836 <tr>
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837 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
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838 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-k">from</span> matplotlib.mlab <span class="pl-k">import</span> <span class="pl-c1">PCA</span></td>
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839 </tr>
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840 <tr>
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841 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
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842 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> seaborn <span class="pl-k">as</span> sns</td>
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843 </tr>
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844 <tr>
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845 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
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846 <td id="LC32" class="blob-code blob-code-inner js-file-line">
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847 </td>
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848 </tr>
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849 <tr>
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850 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
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851 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> some globals for convenience</span></td>
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|
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852 </tr>
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853 <tr>
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854 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
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855 <td id="LC34" class="blob-code blob-code-inner js-file-line">
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856 </td>
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857 </tr>
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858 <tr>
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859 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
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860 <td id="LC35" 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>
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861 </tr>
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862 <tr>
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863 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
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864 <td id="LC36" class="blob-code blob-code-inner js-file-line">
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865 </td>
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866 </tr>
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867 <tr>
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868 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
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|
|
869 <td id="LC37" 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>" >>"+os.path.dirname(os.path.realpath(__file__))+"/log/Vap_log.txt 2>&1"</span></td>
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|
|
870 </tr>
|
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|
871 <tr>
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|
|
872 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
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873 <td id="LC38" class="blob-code blob-code-inner js-file-line">
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874 </td>
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875 </tr>
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876 <tr>
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|
877 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
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|
878 <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">assembleWithVelvet</span>(<span class="pl-smi">name</span>, <span class="pl-smi">kmers</span>, <span class="pl-smi">inslen</span>, <span class="pl-smi">covcut</span>, <span class="pl-smi">fastq1name</span>,<span class="pl-smi">fastq2name</span>):</td>
|
|
|
879 </tr>
|
|
|
880 <tr>
|
|
|
881 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
|
|
|
882 <td id="LC40" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"</span></td>
|
|
|
883 </tr>
|
|
|
884 <tr>
|
|
|
885 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
|
|
|
886 <td id="LC41" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>velveth <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>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span> kmers<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> kmers <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span> -shortPaired -fastq <span class="pl-pds">"</span></span> <span class="pl-k">+</span> fastq1name<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>fastq2name<span class="pl-k">+</span>quietString</td>
|
|
|
887 </tr>
|
|
|
888 <tr>
|
|
|
889 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
|
|
|
890 <td id="LC42" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
|
|
|
891 </tr>
|
|
|
892 <tr>
|
|
|
893 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
|
|
|
894 <td id="LC43" 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>
|
|
|
895 </tr>
|
|
|
896 <tr>
|
|
|
897 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
|
|
|
898 <td id="LC44" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
|
|
|
899 </tr>
|
|
|
900 <tr>
|
|
|
901 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
|
|
|
902 <td id="LC45" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in velveth<span class="pl-pds">"</span></span></td>
|
|
|
903 </tr>
|
|
|
904 <tr>
|
|
|
905 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
|
|
|
906 <td id="LC46" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>velvetg <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>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -exp_cov auto -ins_length <span class="pl-pds">"</span></span><span class="pl-k">+</span>inslen<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -cov_cutoff <span class="pl-pds">"</span></span><span class="pl-k">+</span>covcut<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -clean yes -ins_length_sd 50 -min_pair_count 20<span class="pl-pds">"</span></span><span class="pl-k">+</span>quietString</td>
|
|
|
907 </tr>
|
|
|
908 <tr>
|
|
|
909 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
|
|
|
910 <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString</span></td>
|
|
|
911 </tr>
|
|
|
912 <tr>
|
|
|
913 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
|
|
|
914 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
|
|
|
915 </tr>
|
|
|
916 <tr>
|
|
|
917 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
|
|
|
918 <td id="LC49" 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>
|
|
|
919 </tr>
|
|
|
920 <tr>
|
|
|
921 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
|
|
|
922 <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
|
|
|
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"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in velvetg<span class="pl-pds">"</span></span></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"> shutil.copyfile(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>//contigs.fa<span class="pl-pds">"</span></span>,name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.fa<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span> my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";</span></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"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>ok<span class="pl-pds">"</span></span></td>
|
|
|
935 </tr>
|
|
|
936 <tr>
|
|
|
937 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
|
|
|
938 <td id="LC54" class="blob-code blob-code-inner js-file-line">
|
|
|
939 </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"><span class="pl-k">def</span> <span class="pl-en">contigTranslation</span>(<span class="pl-smi">name</span>):</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"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>transeq <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>.fa <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 -frame=6 <span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span>+quietString</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"> <span class="pl-c1">print</span>(argString)</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"> 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>
|
|
|
956 </tr>
|
|
|
957 <tr>
|
|
|
958 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
|
|
|
959 <td id="LC59" class="blob-code blob-code-inner js-file-line">
|
|
|
960 </td>
|
|
|
961 </tr>
|
|
|
962 <tr>
|
|
|
963 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
|
|
|
964 <td id="LC60" class="blob-code blob-code-inner js-file-line">
|
|
|
965 </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"><span class="pl-k">def</span> <span class="pl-en">HMMerMotifSearch</span>(<span class="pl-smi">name</span>):</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"> 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>
|
|
|
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"> <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>
|
|
|
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"> lineCounts <span class="pl-k">=</span> []</td>
|
|
|
982 </tr>
|
|
|
983 <tr>
|
|
|
984 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
|
|
|
985 <td id="LC65" class="blob-code blob-code-inner js-file-line"> compoundList <span class="pl-k">=</span> []</td>
|
|
|
986 </tr>
|
|
|
987 <tr>
|
|
|
988 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
|
|
|
989 <td id="LC66" 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>
|
|
|
990 </tr>
|
|
|
991 <tr>
|
|
|
992 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
|
|
|
993 <td id="LC67" 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>
|
|
|
994 </tr>
|
|
|
995 <tr>
|
|
|
996 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
|
|
|
997 <td id="LC68" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> m <span class="pl-k">in</span> motifs:</td>
|
|
|
998 </tr>
|
|
|
999 <tr>
|
|
|
1000 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
|
|
|
1001 <td id="LC69" 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> <span class="pl-c"><span class="pl-c">#</span> +quietString</span></td>
|
|
|
1002 </tr>
|
|
|
1003 <tr>
|
|
|
1004 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
|
|
|
1005 <td id="LC70" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> argString = "hmmsearch "+phylopath + m + ".hmm " + dir_path+"/data/Test_6frame.fas > Phy" + m + ".out"</span></td>
|
|
|
1006 </tr>
|
|
|
1007 <tr>
|
|
|
1008 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
|
|
|
1009 <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(argString)</span></td>
|
|
|
1010 </tr>
|
|
|
1011 <tr>
|
|
|
1012 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
|
|
|
1013 <td id="LC72" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1014 </tr>
|
|
|
1015 <tr>
|
|
|
1016 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
|
|
|
1017 <td id="LC73" class="blob-code blob-code-inner js-file-line">
|
|
|
1018 </td>
|
|
|
1019 </tr>
|
|
|
1020 <tr>
|
|
|
1021 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
|
|
|
1022 <td id="LC74" 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>
|
|
|
1023 </tr>
|
|
|
1024 <tr>
|
|
|
1025 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
|
|
|
1026 <td id="LC75" class="blob-code blob-code-inner js-file-line"> tempout <span class="pl-k">=</span> <span class="pl-c1">open</span>(dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/<span class="pl-pds">"</span></span> <span class="pl-k">+</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>.txt<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>)</td>
|
|
|
1027 </tr>
|
|
|
1028 <tr>
|
|
|
1029 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
|
|
|
1030 <td id="LC76" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>regex = r"NODE_[0-9]{1,7}_length_[0-9]{1,7}_cov_[0-9]{1,10}.[0-9]{1,7}_[0-9]{1,2}"</span></td>
|
|
|
1031 </tr>
|
|
|
1032 <tr>
|
|
|
1033 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
|
|
|
1034 <td id="LC77" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1035 </tr>
|
|
|
1036 <tr>
|
|
|
1037 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
|
|
|
1038 <td id="LC78" class="blob-code blob-code-inner js-file-line"> outList <span class="pl-k">=</span> []</td>
|
|
|
1039 </tr>
|
|
|
1040 <tr>
|
|
|
1041 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
|
|
|
1042 <td id="LC79" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> l <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">14</span>):</td>
|
|
|
1043 </tr>
|
|
|
1044 <tr>
|
|
|
1045 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
|
|
|
1046 <td id="LC80" class="blob-code blob-code-inner js-file-line"> hmmResult.readline() <span class="pl-c"><span class="pl-c">#</span>hacky? miss out the first 14 lines. data we want starts on line 15</span></td>
|
|
|
1047 </tr>
|
|
|
1048 <tr>
|
|
|
1049 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
|
|
|
1050 <td id="LC81" class="blob-code blob-code-inner js-file-line">
|
|
|
1051 </td>
|
|
|
1052 </tr>
|
|
|
1053 <tr>
|
|
|
1054 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
|
|
|
1055 <td id="LC82" class="blob-code blob-code-inner js-file-line">
|
|
|
1056 </td>
|
|
|
1057 </tr>
|
|
|
1058 <tr>
|
|
|
1059 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
|
|
|
1060 <td id="LC83" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> line <span class="pl-k">in</span> hmmResult:</td>
|
|
|
1061 </tr>
|
|
|
1062 <tr>
|
|
|
1063 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
|
|
|
1064 <td id="LC84" 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>
|
|
|
1065 </tr>
|
|
|
1066 <tr>
|
|
|
1067 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
|
|
|
1068 <td id="LC85" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("inclusion threshold reached")</span></td>
|
|
|
1069 </tr>
|
|
|
1070 <tr>
|
|
|
1071 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
|
|
|
1072 <td id="LC86" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span></td>
|
|
|
1073 </tr>
|
|
|
1074 <tr>
|
|
|
1075 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
|
|
|
1076 <td id="LC87" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-c1">len</span>(line) <span class="pl-k"><=</span> <span class="pl-c1">1</span>:</td>
|
|
|
1077 </tr>
|
|
|
1078 <tr>
|
|
|
1079 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
|
|
|
1080 <td id="LC88" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("end of data")</span></td>
|
|
|
1081 </tr>
|
|
|
1082 <tr>
|
|
|
1083 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
|
|
|
1084 <td id="LC89" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span></td>
|
|
|
1085 </tr>
|
|
|
1086 <tr>
|
|
|
1087 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
|
|
|
1088 <td id="LC90" class="blob-code blob-code-inner js-file-line"> m <span class="pl-k">=</span> line[<span class="pl-c1">60</span>:<span class="pl-k">-</span><span class="pl-c1">1</span>]</td>
|
|
|
1089 </tr>
|
|
|
1090 <tr>
|
|
|
1091 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
|
|
|
1092 <td id="LC91" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(m)</span></td>
|
|
|
1093 </tr>
|
|
|
1094 <tr>
|
|
|
1095 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
|
|
|
1096 <td id="LC92" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>tempout.write(m.group() + "\n")</span></td>
|
|
|
1097 </tr>
|
|
|
1098 <tr>
|
|
|
1099 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
|
|
|
1100 <td id="LC93" 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 <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>)</td>
|
|
|
1101 </tr>
|
|
|
1102 <tr>
|
|
|
1103 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
|
|
|
1104 <td id="LC94" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">+=</span> <span class="pl-c1">1</span></td>
|
|
|
1105 </tr>
|
|
|
1106 <tr>
|
|
|
1107 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
|
|
|
1108 <td id="LC95" class="blob-code blob-code-inner js-file-line"> compoundList.append(outList)</td>
|
|
|
1109 </tr>
|
|
|
1110 <tr>
|
|
|
1111 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
|
|
|
1112 <td id="LC96" class="blob-code blob-code-inner js-file-line"> lineCounts.append(n)</td>
|
|
|
1113 </tr>
|
|
|
1114 <tr>
|
|
|
1115 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
|
|
|
1116 <td id="LC97" class="blob-code blob-code-inner js-file-line"> hmmResult.close()</td>
|
|
|
1117 </tr>
|
|
|
1118 <tr>
|
|
|
1119 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
|
|
|
1120 <td id="LC98" class="blob-code blob-code-inner js-file-line">
|
|
|
1121 </td>
|
|
|
1122 </tr>
|
|
|
1123 <tr>
|
|
|
1124 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
|
|
|
1125 <td id="LC99" class="blob-code blob-code-inner js-file-line">
|
|
|
1126 </td>
|
|
|
1127 </tr>
|
|
|
1128 <tr>
|
|
|
1129 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
|
|
|
1130 <td id="LC100" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(lineCounts)</td>
|
|
|
1131 </tr>
|
|
|
1132 <tr>
|
|
|
1133 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
|
|
|
1134 <td id="LC101" class="blob-code blob-code-inner js-file-line"> motifGroups <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>
|
|
|
1135 </tr>
|
|
|
1136 <tr>
|
|
|
1137 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
|
|
|
1138 <td id="LC102" 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>],</td>
|
|
|
1139 </tr>
|
|
|
1140 <tr>
|
|
|
1141 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
|
|
|
1142 <td id="LC103" class="blob-code blob-code-inner js-file-line"> [<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>
|
|
|
1143 </tr>
|
|
|
1144 <tr>
|
|
|
1145 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
|
|
|
1146 <td id="LC104" 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>
|
|
|
1147 </tr>
|
|
|
1148 <tr>
|
|
|
1149 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
|
|
|
1150 <td id="LC105" class="blob-code blob-code-inner js-file-line"> countList <span class="pl-k">=</span> []</td>
|
|
|
1151 </tr>
|
|
|
1152 <tr>
|
|
|
1153 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
|
|
|
1154 <td id="LC106" class="blob-code blob-code-inner js-file-line"> countIndex <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1155 </tr>
|
|
|
1156 <tr>
|
|
|
1157 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
|
|
|
1158 <td id="LC107" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1159 </tr>
|
|
|
1160 <tr>
|
|
|
1161 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
|
|
|
1162 <td id="LC108" class="blob-code blob-code-inner js-file-line">
|
|
|
1163 </td>
|
|
|
1164 </tr>
|
|
|
1165 <tr>
|
|
|
1166 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
|
|
|
1167 <td id="LC109" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> c <span class="pl-k">in</span> concatGroups:</td>
|
|
|
1168 </tr>
|
|
|
1169 <tr>
|
|
|
1170 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
|
|
|
1171 <td id="LC110" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> []</td>
|
|
|
1172 </tr>
|
|
|
1173 <tr>
|
|
|
1174 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
|
|
|
1175 <td id="LC111" 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>
|
|
|
1176 </tr>
|
|
|
1177 <tr>
|
|
|
1178 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
|
|
|
1179 <td id="LC112" 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>
|
|
|
1180 </tr>
|
|
|
1181 <tr>
|
|
|
1182 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
|
|
|
1183 <td id="LC113" class="blob-code blob-code-inner js-file-line"> t <span class="pl-k">=</span> <span class="pl-c1">set</span>(a)</td>
|
|
|
1184 </tr>
|
|
|
1185 <tr>
|
|
|
1186 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
|
|
|
1187 <td id="LC114" class="blob-code blob-code-inner js-file-line"> countList.append(<span class="pl-c1">len</span>(t))</td>
|
|
|
1188 </tr>
|
|
|
1189 <tr>
|
|
|
1190 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
|
|
|
1191 <td id="LC115" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">+=</span> <span class="pl-c1">len</span>(t)</td>
|
|
|
1192 </tr>
|
|
|
1193 <tr>
|
|
|
1194 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
|
|
|
1195 <td id="LC116" class="blob-code blob-code-inner js-file-line"> countList.append(totalCount)</td>
|
|
|
1196 </tr>
|
|
|
1197 <tr>
|
|
|
1198 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
|
|
|
1199 <td id="LC117" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(countList)</span></td>
|
|
|
1200 </tr>
|
|
|
1201 <tr>
|
|
|
1202 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
|
|
|
1203 <td id="LC118" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("--------")</span></td>
|
|
|
1204 </tr>
|
|
|
1205 <tr>
|
|
|
1206 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
|
|
|
1207 <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> countList</td>
|
|
|
1208 </tr>
|
|
|
1209 <tr>
|
|
|
1210 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
|
|
|
1211 <td id="LC120" class="blob-code blob-code-inner js-file-line">
|
|
|
1212 </td>
|
|
|
1213 </tr>
|
|
|
1214 <tr>
|
|
|
1215 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
|
|
|
1216 <td id="LC121" class="blob-code blob-code-inner js-file-line">
|
|
|
1217 </td>
|
|
|
1218 </tr>
|
|
|
1219 <tr>
|
|
|
1220 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
|
|
|
1221 <td id="LC122" class="blob-code blob-code-inner js-file-line">
|
|
|
1222 </td>
|
|
|
1223 </tr>
|
|
|
1224 <tr>
|
|
|
1225 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
|
|
|
1226 <td id="LC123" 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>
|
|
|
1227 </tr>
|
|
|
1228 <tr>
|
|
|
1229 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
|
|
|
1230 <td id="LC124" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td>
|
|
|
1231 </tr>
|
|
|
1232 <tr>
|
|
|
1233 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
|
|
|
1234 <td id="LC125" 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>
|
|
|
1235 </tr>
|
|
|
1236 <tr>
|
|
|
1237 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
|
|
|
1238 <td id="LC126" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> c <span class="pl-k">==</span> <span class="pl-c1">0</span>:</td>
|
|
|
1239 </tr>
|
|
|
1240 <tr>
|
|
|
1241 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
|
|
|
1242 <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> [<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>, <span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>, <span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>]</td>
|
|
|
1243 </tr>
|
|
|
1244 <tr>
|
|
|
1245 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
|
|
|
1246 <td id="LC128" 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>
|
|
|
1247 </tr>
|
|
|
1248 <tr>
|
|
|
1249 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
|
|
|
1250 <td id="LC129" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td>
|
|
|
1251 </tr>
|
|
|
1252 <tr>
|
|
|
1253 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
|
|
|
1254 <td id="LC130" class="blob-code blob-code-inner js-file-line">
|
|
|
1255 </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"> 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>
|
|
|
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"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</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"> 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>_relative_frequency.csv<span class="pl-pds">"</span></span></td>
|
|
|
1268 </tr>
|
|
|
1269 <tr>
|
|
|
1270 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
|
|
|
1271 <td id="LC134" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</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> relFreqList <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></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">
|
|
|
1285 </td>
|
|
|
1286 </tr>
|
|
|
1287 <tr>
|
|
|
1288 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
|
|
|
1289 <td id="LC138" class="blob-code blob-code-inner js-file-line">
|
|
|
1290 </td>
|
|
|
1291 </tr>
|
|
|
1292 <tr>
|
|
|
1293 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
|
|
|
1294 <td id="LC139" class="blob-code blob-code-inner js-file-line">
|
|
|
1295 </td>
|
|
|
1296 </tr>
|
|
|
1297 <tr>
|
|
|
1298 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
|
|
|
1299 <td id="LC140" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getDeviationFromMean</span>(<span class="pl-smi">frequencyList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td>
|
|
|
1300 </tr>
|
|
|
1301 <tr>
|
|
|
1302 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
|
|
|
1303 <td id="LC141" class="blob-code blob-code-inner js-file-line"> devList <span class="pl-k">=</span> []</td>
|
|
|
1304 </tr>
|
|
|
1305 <tr>
|
|
|
1306 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
|
|
|
1307 <td id="LC142" 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>
|
|
|
1308 </tr>
|
|
|
1309 <tr>
|
|
|
1310 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
|
|
|
1311 <td id="LC143" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/congodata.csv<span class="pl-pds">"</span></span></td>
|
|
|
1312 </tr>
|
|
|
1313 <tr>
|
|
|
1314 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
|
|
|
1315 <td id="LC144" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>j_fname = r"data/congodata.csv"</span></td>
|
|
|
1316 </tr>
|
|
|
1317 <tr>
|
|
|
1318 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
|
|
|
1319 <td id="LC145" class="blob-code blob-code-inner js-file-line"> congo_df <span class="pl-k">=</span> pd.read_csv(j_fname) <span class="pl-c"><span class="pl-c">#</span> we get the means from congo_df</span></td>
|
|
|
1320 </tr>
|
|
|
1321 <tr>
|
|
|
1322 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
|
|
|
1323 <td id="LC146" 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>
|
|
|
1324 </tr>
|
|
|
1325 <tr>
|
|
|
1326 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
|
|
|
1327 <td id="LC147" class="blob-code blob-code-inner js-file-line"> m <span class="pl-k">=</span> congo_df[pList[p]].mean()</td>
|
|
|
1328 </tr>
|
|
|
1329 <tr>
|
|
|
1330 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
|
|
|
1331 <td id="LC148" class="blob-code blob-code-inner js-file-line"> dev <span class="pl-k">=</span> <span class="pl-k">-</span>(m <span class="pl-k">-</span> frequencyList[p])</td>
|
|
|
1332 </tr>
|
|
|
1333 <tr>
|
|
|
1334 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
|
|
|
1335 <td id="LC149" class="blob-code blob-code-inner js-file-line"> devList.append(dev)</td>
|
|
|
1336 </tr>
|
|
|
1337 <tr>
|
|
|
1338 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
|
|
|
1339 <td id="LC150" class="blob-code blob-code-inner js-file-line">
|
|
|
1340 </td>
|
|
|
1341 </tr>
|
|
|
1342 <tr>
|
|
|
1343 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
|
|
|
1344 <td id="LC151" 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>Deviation from Mean<span class="pl-pds">'</span></span>: devList}</td>
|
|
|
1345 </tr>
|
|
|
1346 <tr>
|
|
|
1347 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
|
|
|
1348 <td id="LC152" class="blob-code blob-code-inner js-file-line"> dev_df <span class="pl-k">=</span> pd.DataFrame(data)</td>
|
|
|
1349 </tr>
|
|
|
1350 <tr>
|
|
|
1351 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
|
|
|
1352 <td id="LC153" 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>_deviation_from_mean.csv<span class="pl-pds">"</span></span></td>
|
|
|
1353 </tr>
|
|
|
1354 <tr>
|
|
|
1355 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
|
|
|
1356 <td id="LC154" class="blob-code blob-code-inner js-file-line"> dev_df.to_csv(j_fname)</td>
|
|
|
1357 </tr>
|
|
|
1358 <tr>
|
|
|
1359 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
|
|
|
1360 <td id="LC155" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> devList</td>
|
|
|
1361 </tr>
|
|
|
1362 <tr>
|
|
|
1363 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
|
|
|
1364 <td id="LC156" class="blob-code blob-code-inner js-file-line">
|
|
|
1365 </td>
|
|
|
1366 </tr>
|
|
|
1367 <tr>
|
|
|
1368 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
|
|
|
1369 <td id="LC157" class="blob-code blob-code-inner js-file-line">
|
|
|
1370 </td>
|
|
|
1371 </tr>
|
|
|
1372 <tr>
|
|
|
1373 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
|
|
|
1374 <td id="LC158" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">relativeFrequencyHeatMap</span>(<span class="pl-smi">name</span>, <span class="pl-smi">freqList</span>, <span class="pl-smi">pdf</span>, <span class="pl-smi">htmlresource</span>):</td>
|
|
|
1375 </tr>
|
|
|
1376 <tr>
|
|
|
1377 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
|
|
|
1378 <td id="LC159" class="blob-code blob-code-inner js-file-line"> localFreqList <span class="pl-k">=</span> freqList[:]</td>
|
|
|
1379 </tr>
|
|
|
1380 <tr>
|
|
|
1381 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
|
|
|
1382 <td id="LC160" class="blob-code blob-code-inner js-file-line"> localFreqList.insert(<span class="pl-c1">0</span>, name)</td>
|
|
|
1383 </tr>
|
|
|
1384 <tr>
|
|
|
1385 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
|
|
|
1386 <td id="LC161" 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>
|
|
|
1387 </tr>
|
|
|
1388 <tr>
|
|
|
1389 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
|
|
|
1390 <td id="LC162" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/data/congodata.csv<span class="pl-pds">"</span></span></td>
|
|
|
1391 </tr>
|
|
|
1392 <tr>
|
|
|
1393 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
|
|
|
1394 <td id="LC163" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(dir_path)</span></td>
|
|
|
1395 </tr>
|
|
|
1396 <tr>
|
|
|
1397 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
|
|
|
1398 <td id="LC164" class="blob-code blob-code-inner js-file-line"> congo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
|
|
|
1399 </tr>
|
|
|
1400 <tr>
|
|
|
1401 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
|
|
|
1402 <td id="LC165" class="blob-code blob-code-inner js-file-line"> congo_df.drop(<span class="pl-s"><span class="pl-pds">'</span>Colour<span class="pl-pds">'</span></span>, <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1403 </tr>
|
|
|
1404 <tr>
|
|
|
1405 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
|
|
|
1406 <td id="LC166" class="blob-code blob-code-inner js-file-line"> congo_df.loc[congo_df.index.max() <span class="pl-k">+</span> <span class="pl-c1">1</span>] <span class="pl-k">=</span> localFreqList</td>
|
|
|
1407 </tr>
|
|
|
1408 <tr>
|
|
|
1409 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
|
|
|
1410 <td id="LC167" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(congo_df) <span class="pl-k">*</span> <span class="pl-c1">20</span> <span class="pl-k">/</span> <span class="pl-c1">97.0</span> <span class="pl-c"><span class="pl-c">#</span> make vertical size equivlanet 20' is ok for 97.</span></td>
|
|
|
1411 </tr>
|
|
|
1412 <tr>
|
|
|
1413 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
|
|
|
1414 <td id="LC168" class="blob-code blob-code-inner js-file-line">
|
|
|
1415 </td>
|
|
|
1416 </tr>
|
|
|
1417 <tr>
|
|
|
1418 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
|
|
|
1419 <td id="LC169" class="blob-code blob-code-inner js-file-line"> congo_df.set_index(<span class="pl-s"><span class="pl-pds">'</span>Strain<span class="pl-pds">'</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1420 </tr>
|
|
|
1421 <tr>
|
|
|
1422 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
|
|
|
1423 <td id="LC170" class="blob-code blob-code-inner js-file-line">
|
|
|
1424 </td>
|
|
|
1425 </tr>
|
|
|
1426 <tr>
|
|
|
1427 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
|
|
|
1428 <td id="LC171" class="blob-code blob-code-inner js-file-line"> cg <span class="pl-k">=</span> sns.clustermap(congo_df, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>ward<span class="pl-pds">'</span></span>, <span class="pl-v">cmap</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>RdBu_r<span class="pl-pds">"</span></span>, <span class="pl-v">col_cluster</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">yticklabels</span> <span class="pl-k">=</span> congo_df.index.values,<span class="pl-v">figsize</span> <span class="pl-k">=</span> (<span class="pl-c1">10</span>,ysize))</td>
|
|
|
1429 </tr>
|
|
|
1430 <tr>
|
|
|
1431 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
|
|
|
1432 <td id="LC172" class="blob-code blob-code-inner js-file-line"> plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), <span class="pl-v">rotation</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">fontsize</span><span class="pl-k">=</span><span class="pl-c1">8</span>) <span class="pl-c"><span class="pl-c">#</span> get y labels printed horizontally</span></td>
|
|
|
1433 </tr>
|
|
|
1434 <tr>
|
|
|
1435 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
|
|
|
1436 <td id="LC173" class="blob-code blob-code-inner js-file-line"> ax<span class="pl-k">=</span>cg.ax_heatmap</td>
|
|
|
1437 </tr>
|
|
|
1438 <tr>
|
|
|
1439 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
|
|
|
1440 <td id="LC174" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$ estimated as the phylotype proportion across the<span class="pl-cce">\n</span>sample cohort. <span class="pl-pds">"</span></span></td>
|
|
|
1441 </tr>
|
|
|
1442 <tr>
|
|
|
1443 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
|
|
|
1444 <td id="LC175" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span>Dendrogram reflects the relationships amongst the VSG repertoires of each strain. <span class="pl-pds">"</span></span></td>
|
|
|
1445 </tr>
|
|
|
1446 <tr>
|
|
|
1447 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
|
|
|
1448 <td id="LC176" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span>Strains<span class="pl-cce">\n</span>were isolated from multiple African countries as described in Silva Pereira et al. (2018).<span class="pl-pds">"</span></span></td>
|
|
|
1449 </tr>
|
|
|
1450 <tr>
|
|
|
1451 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
|
|
|
1452 <td id="LC177" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span> <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>
|
|
|
1453 </tr>
|
|
|
1454 <tr>
|
|
|
1455 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
|
|
|
1456 <td id="LC178" class="blob-code blob-code-inner js-file-line">
|
|
|
1457 </td>
|
|
|
1458 </tr>
|
|
|
1459 <tr>
|
|
|
1460 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
|
|
|
1461 <td id="LC179" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>title = "Variant Antigen Profiles of Trypanosoma congolense estimated as the phylotype proportion across the sample cohort. Dendrogram reflects the relationships amongst the VSG repertoires of each strain. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018). Data was produced with the 'Variant Antigen Profiler' (Silva Pereira and Jackson, 2018)."</span></td>
|
|
|
1462 </tr>
|
|
|
1463 <tr>
|
|
|
1464 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
|
|
|
1465 <td id="LC180" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ax.set_title(title, ha = "center", va = "bottom",wrap = "True")</span></td>
|
|
|
1466 </tr>
|
|
|
1467 <tr>
|
|
|
1468 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
|
|
|
1469 <td id="LC181" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>title = "Where is this!"</span></td>
|
|
|
1470 </tr>
|
|
|
1471 <tr>
|
|
|
1472 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
|
|
|
1473 <td id="LC182" class="blob-code blob-code-inner js-file-line"> ax.text(<span class="pl-k">-</span><span class="pl-c1">0.15</span>,<span class="pl-k">-</span><span class="pl-c1">0.05</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>, <span class="pl-v">transform</span> <span class="pl-k">=</span> ax.transAxes )</td>
|
|
|
1474 </tr>
|
|
|
1475 <tr>
|
|
|
1476 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
|
|
|
1477 <td id="LC183" class="blob-code blob-code-inner js-file-line">
|
|
|
1478 </td>
|
|
|
1479 </tr>
|
|
|
1480 <tr>
|
|
|
1481 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
|
|
|
1482 <td id="LC184" class="blob-code blob-code-inner js-file-line">
|
|
|
1483 </td>
|
|
|
1484 </tr>
|
|
|
1485 <tr>
|
|
|
1486 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
|
|
|
1487 <td id="LC185" class="blob-code blob-code-inner js-file-line">
|
|
|
1488 </td>
|
|
|
1489 </tr>
|
|
|
1490 <tr>
|
|
|
1491 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
|
|
|
1492 <td id="LC186" class="blob-code blob-code-inner js-file-line">
|
|
|
1493 </td>
|
|
|
1494 </tr>
|
|
|
1495 <tr>
|
|
|
1496 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
|
|
|
1497 <td id="LC187" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_col.linkage # linkage matrix for columns</span></td>
|
|
|
1498 </tr>
|
|
|
1499 <tr>
|
|
|
1500 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
|
|
|
1501 <td id="LC188" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_row.linkage # linkage matrix for rows</span></td>
|
|
|
1502 </tr>
|
|
|
1503 <tr>
|
|
|
1504 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
|
|
|
1505 <td id="LC189" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.savefig(r"results/" + name + "_heatmap.png")</span></td>
|
|
|
1506 </tr>
|
|
|
1507 <tr>
|
|
|
1508 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
|
|
|
1509 <td id="LC190" class="blob-code blob-code-inner js-file-line"> plt.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/heatmap.png<span class="pl-pds">"</span></span>,<span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>tight<span class="pl-pds">'</span></span>)</td>
|
|
|
1510 </tr>
|
|
|
1511 <tr>
|
|
|
1512 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
|
|
|
1513 <td id="LC191" 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>
|
|
|
1514 </tr>
|
|
|
1515 <tr>
|
|
|
1516 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
|
|
|
1517 <td id="LC192" class="blob-code blob-code-inner js-file-line"> plt.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/heatmap.pdf<span class="pl-pds">"</span></span>, <span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>tight<span class="pl-pds">'</span></span>)</td>
|
|
|
1518 </tr>
|
|
|
1519 <tr>
|
|
|
1520 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
|
|
|
1521 <td id="LC193" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>shutil.copyfile("heatmap.pdf",heatmapfn) #</span></td>
|
|
|
1522 </tr>
|
|
|
1523 <tr>
|
|
|
1524 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
|
|
|
1525 <td id="LC194" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
|
|
|
1526 </tr>
|
|
|
1527 <tr>
|
|
|
1528 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
|
|
|
1529 <td id="LC195" class="blob-code blob-code-inner js-file-line">
|
|
|
1530 </td>
|
|
|
1531 </tr>
|
|
|
1532 <tr>
|
|
|
1533 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
|
|
|
1534 <td id="LC196" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">deviationFromMeanHeatMap</span>(<span class="pl-smi">name</span>,<span class="pl-smi">devList</span>, <span class="pl-smi">pdf</span>, <span class="pl-smi">htmlresource</span>):</td>
|
|
|
1535 </tr>
|
|
|
1536 <tr>
|
|
|
1537 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
|
|
|
1538 <td id="LC197" class="blob-code blob-code-inner js-file-line"> localDevList <span class="pl-k">=</span> devList[:]</td>
|
|
|
1539 </tr>
|
|
|
1540 <tr>
|
|
|
1541 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
|
|
|
1542 <td id="LC198" class="blob-code blob-code-inner js-file-line"> localDevList.insert(<span class="pl-c1">0</span>, name)</td>
|
|
|
1543 </tr>
|
|
|
1544 <tr>
|
|
|
1545 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
|
|
|
1546 <td id="LC199" 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>
|
|
|
1547 </tr>
|
|
|
1548 <tr>
|
|
|
1549 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
|
|
|
1550 <td id="LC200" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path<span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/congodata_deviationfromthemean.csv<span class="pl-pds">"</span></span></td>
|
|
|
1551 </tr>
|
|
|
1552 <tr>
|
|
|
1553 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
|
|
|
1554 <td id="LC201" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>j_fname = r"data/congodata_deviationfromthemean.csv"</span></td>
|
|
|
1555 </tr>
|
|
|
1556 <tr>
|
|
|
1557 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
|
|
|
1558 <td id="LC202" class="blob-code blob-code-inner js-file-line"> congo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
|
|
|
1559 </tr>
|
|
|
1560 <tr>
|
|
|
1561 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
|
|
|
1562 <td id="LC203" class="blob-code blob-code-inner js-file-line"> congo_df.drop(<span class="pl-s"><span class="pl-pds">'</span>Colour<span class="pl-pds">'</span></span>, <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1563 </tr>
|
|
|
1564 <tr>
|
|
|
1565 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
|
|
|
1566 <td id="LC204" class="blob-code blob-code-inner js-file-line"> congo_df.loc[congo_df.index.max() <span class="pl-k">+</span> <span class="pl-c1">1</span>] <span class="pl-k">=</span> localDevList</td>
|
|
|
1567 </tr>
|
|
|
1568 <tr>
|
|
|
1569 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
|
|
|
1570 <td id="LC205" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(congo_df) <span class="pl-k">*</span> <span class="pl-c1">20</span> <span class="pl-k">/</span> <span class="pl-c1">97.0</span> <span class="pl-c"><span class="pl-c">#</span> make vertical size equivlanet 20' is ok for 97.</span></td>
|
|
|
1571 </tr>
|
|
|
1572 <tr>
|
|
|
1573 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
|
|
|
1574 <td id="LC206" class="blob-code blob-code-inner js-file-line"> congo_df.set_index(<span class="pl-s"><span class="pl-pds">'</span>Strain<span class="pl-pds">'</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1575 </tr>
|
|
|
1576 <tr>
|
|
|
1577 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
|
|
|
1578 <td id="LC207" class="blob-code blob-code-inner js-file-line"> cg <span class="pl-k">=</span> sns.clustermap(congo_df, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>ward<span class="pl-pds">'</span></span>,<span class="pl-v">cmap</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>RdBu_r<span class="pl-pds">"</span></span>, <span class="pl-v">col_cluster</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">yticklabels</span> <span class="pl-k">=</span> congo_df.index.values,<span class="pl-v">figsize</span> <span class="pl-k">=</span> (<span class="pl-c1">10</span>,ysize))</td>
|
|
|
1579 </tr>
|
|
|
1580 <tr>
|
|
|
1581 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
|
|
|
1582 <td id="LC208" class="blob-code blob-code-inner js-file-line"> plt.setp(cg.ax_heatmap.yaxis.get_majorticklabels(), <span class="pl-v">rotation</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">fontsize</span><span class="pl-k">=</span><span class="pl-c1">8</span>) <span class="pl-c"><span class="pl-c">#</span> get y labels printed horizontally</span></td>
|
|
|
1583 </tr>
|
|
|
1584 <tr>
|
|
|
1585 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
|
|
|
1586 <td id="LC209" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td>
|
|
|
1587 </tr>
|
|
|
1588 <tr>
|
|
|
1589 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
|
|
|
1590 <td id="LC210" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$ expressed as the deviation from the mean phylotypes <span class="pl-pds">"</span></span></td>
|
|
|
1591 </tr>
|
|
|
1592 <tr>
|
|
|
1593 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
|
|
|
1594 <td id="LC211" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span><span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>proportions of the sample cohort. Dendrogram reflects the relationships amongst the VSG repertoires of <span class="pl-pds">"</span></span></td>
|
|
|
1595 </tr>
|
|
|
1596 <tr>
|
|
|
1597 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
|
|
|
1598 <td id="LC212" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span><span class="pl-s"><span class="pl-pds">"</span>each <span class="pl-cce">\n</span>strain. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018).<span class="pl-pds">"</span></span></td>
|
|
|
1599 </tr>
|
|
|
1600 <tr>
|
|
|
1601 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
|
|
|
1602 <td id="LC213" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span><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>
|
|
|
1603 </tr>
|
|
|
1604 <tr>
|
|
|
1605 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
|
|
|
1606 <td id="LC214" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ax.set_title(title,ha = "center", va = "bottom",wrap = "True")</span></td>
|
|
|
1607 </tr>
|
|
|
1608 <tr>
|
|
|
1609 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
|
|
|
1610 <td id="LC215" class="blob-code blob-code-inner js-file-line"> ax.text(<span class="pl-k">-</span><span class="pl-c1">0.2</span>, <span class="pl-k">-</span><span class="pl-c1">0.05</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">transform</span><span class="pl-k">=</span>ax.transAxes, <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>
|
|
|
1611 </tr>
|
|
|
1612 <tr>
|
|
|
1613 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
|
|
|
1614 <td id="LC216" class="blob-code blob-code-inner js-file-line"> plt.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/dheatmap.png<span class="pl-pds">"</span></span>,<span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>tight<span class="pl-pds">'</span></span>)</td>
|
|
|
1615 </tr>
|
|
|
1616 <tr>
|
|
|
1617 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
|
|
|
1618 <td id="LC217" 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>
|
|
|
1619 </tr>
|
|
|
1620 <tr>
|
|
|
1621 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
|
|
|
1622 <td id="LC218" class="blob-code blob-code-inner js-file-line"> plt.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/dheatmap.pdf<span class="pl-pds">"</span></span>, <span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>tight<span class="pl-pds">'</span></span>)</td>
|
|
|
1623 </tr>
|
|
|
1624 <tr>
|
|
|
1625 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
|
|
|
1626 <td id="LC219" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>shutil.copyfile("dheatmap.pdf",dhmapfn)</span></td>
|
|
|
1627 </tr>
|
|
|
1628 <tr>
|
|
|
1629 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
|
|
|
1630 <td id="LC220" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
|
|
|
1631 </tr>
|
|
|
1632 <tr>
|
|
|
1633 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
|
|
|
1634 <td id="LC221" class="blob-code blob-code-inner js-file-line">
|
|
|
1635 </td>
|
|
|
1636 </tr>
|
|
|
1637 <tr>
|
|
|
1638 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
|
|
|
1639 <td id="LC222" class="blob-code blob-code-inner js-file-line">
|
|
|
1640 </td>
|
|
|
1641 </tr>
|
|
|
1642 <tr>
|
|
|
1643 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
|
|
|
1644 <td id="LC223" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">plotPCA</span>(<span class="pl-smi">name</span>, <span class="pl-smi">freqList</span>, <span class="pl-smi">pdf</span>, <span class="pl-smi">htmlresource</span>):</td>
|
|
|
1645 </tr>
|
|
|
1646 <tr>
|
|
|
1647 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
|
|
|
1648 <td id="LC224" class="blob-code blob-code-inner js-file-line"> localFreqList <span class="pl-k">=</span> freqList[:]</td>
|
|
|
1649 </tr>
|
|
|
1650 <tr>
|
|
|
1651 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
|
|
|
1652 <td id="LC225" class="blob-code blob-code-inner js-file-line"> localFreqList.insert(<span class="pl-c1">0</span>, name)</td>
|
|
|
1653 </tr>
|
|
|
1654 <tr>
|
|
|
1655 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
|
|
|
1656 <td id="LC226" class="blob-code blob-code-inner js-file-line"> localFreqList.append(name)</td>
|
|
|
1657 </tr>
|
|
|
1658 <tr>
|
|
|
1659 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
|
|
|
1660 <td id="LC227" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
|
|
|
1661 </tr>
|
|
|
1662 <tr>
|
|
|
1663 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
|
|
|
1664 <td id="LC228" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/congodata.csv<span class="pl-pds">"</span></span></td>
|
|
|
1665 </tr>
|
|
|
1666 <tr>
|
|
|
1667 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
|
|
|
1668 <td id="LC229" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>j_fname = r"data/congodata.csv"</span></td>
|
|
|
1669 </tr>
|
|
|
1670 <tr>
|
|
|
1671 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
|
|
|
1672 <td id="LC230" class="blob-code blob-code-inner js-file-line"> congo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
|
|
|
1673 </tr>
|
|
|
1674 <tr>
|
|
|
1675 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
|
|
|
1676 <td id="LC231" class="blob-code blob-code-inner js-file-line"> congo_df.loc[congo_df.index.max() <span class="pl-k">+</span> <span class="pl-c1">1</span>] <span class="pl-k">=</span> localFreqList</td>
|
|
|
1677 </tr>
|
|
|
1678 <tr>
|
|
|
1679 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
|
|
|
1680 <td id="LC232" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(congo_df.tail(2))</span></td>
|
|
|
1681 </tr>
|
|
|
1682 <tr>
|
|
|
1683 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
|
|
|
1684 <td id="LC233" class="blob-code blob-code-inner js-file-line"> myColours <span class="pl-k">=</span> congo_df[<span class="pl-s"><span class="pl-pds">'</span>Colour<span class="pl-pds">'</span></span>]</td>
|
|
|
1685 </tr>
|
|
|
1686 <tr>
|
|
|
1687 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
|
|
|
1688 <td id="LC234" class="blob-code blob-code-inner js-file-line"> myCountries <span class="pl-k">=</span> congo_df.drop_duplicates(<span class="pl-s"><span class="pl-pds">'</span>Colour<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>Colour<span class="pl-pds">'</span></span>].tolist()</td>
|
|
|
1689 </tr>
|
|
|
1690 <tr>
|
|
|
1691 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
|
|
|
1692 <td id="LC235" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(myCountries)</span></td>
|
|
|
1693 </tr>
|
|
|
1694 <tr>
|
|
|
1695 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
|
|
|
1696 <td id="LC236" class="blob-code blob-code-inner js-file-line"> congo_df.drop(<span class="pl-s"><span class="pl-pds">'</span>Colour<span class="pl-pds">'</span></span>, <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1697 </tr>
|
|
|
1698 <tr>
|
|
|
1699 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
|
|
|
1700 <td id="LC237" class="blob-code blob-code-inner js-file-line"> congo_df.set_index(<span class="pl-s"><span class="pl-pds">'</span>Strain<span class="pl-pds">'</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
|
1701 </tr>
|
|
|
1702 <tr>
|
|
|
1703 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
|
|
|
1704 <td id="LC238" class="blob-code blob-code-inner js-file-line"> dataArray <span class="pl-k">=</span> congo_df.as_matrix()</td>
|
|
|
1705 </tr>
|
|
|
1706 <tr>
|
|
|
1707 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
|
|
|
1708 <td id="LC239" class="blob-code blob-code-inner js-file-line"> pcaResult <span class="pl-k">=</span> PCA(dataArray)</td>
|
|
|
1709 </tr>
|
|
|
1710 <tr>
|
|
|
1711 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
|
|
|
1712 <td id="LC240" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> pcaResult.center(0)</span></td>
|
|
|
1713 </tr>
|
|
|
1714 <tr>
|
|
|
1715 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
|
|
|
1716 <td id="LC241" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> can't seem to find a simple way of prooducing a decent legend.</span></td>
|
|
|
1717 </tr>
|
|
|
1718 <tr>
|
|
|
1719 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
|
|
|
1720 <td id="LC242" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> going to seperate items in to different countires.</span></td>
|
|
|
1721 </tr>
|
|
|
1722 <tr>
|
|
|
1723 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
|
|
|
1724 <td id="LC243" class="blob-code blob-code-inner js-file-line"> compoundList <span class="pl-k">=</span> []</td>
|
|
|
1725 </tr>
|
|
|
1726 <tr>
|
|
|
1727 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
|
|
|
1728 <td id="LC244" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> myCountries:</td>
|
|
|
1729 </tr>
|
|
|
1730 <tr>
|
|
|
1731 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
|
|
|
1732 <td id="LC245" class="blob-code blob-code-inner js-file-line"> compoundList.append([])</td>
|
|
|
1733 </tr>
|
|
|
1734 <tr>
|
|
|
1735 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
|
|
|
1736 <td id="LC246" class="blob-code blob-code-inner js-file-line">
|
|
|
1737 </td>
|
|
|
1738 </tr>
|
|
|
1739 <tr>
|
|
|
1740 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
|
|
|
1741 <td id="LC247" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1742 </tr>
|
|
|
1743 <tr>
|
|
|
1744 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
|
|
|
1745 <td id="LC248" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> item <span class="pl-k">in</span> pcaResult.Y:</td>
|
|
|
1746 </tr>
|
|
|
1747 <tr>
|
|
|
1748 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
|
|
|
1749 <td id="LC249" class="blob-code blob-code-inner js-file-line"> col <span class="pl-k">=</span> myCountries.index(myColours[i])</td>
|
|
|
1750 </tr>
|
|
|
1751 <tr>
|
|
|
1752 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
|
|
|
1753 <td id="LC250" class="blob-code blob-code-inner js-file-line"> compoundList[col].append(<span class="pl-k">-</span>item[<span class="pl-c1">0</span>])</td>
|
|
|
1754 </tr>
|
|
|
1755 <tr>
|
|
|
1756 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
|
|
|
1757 <td id="LC251" class="blob-code blob-code-inner js-file-line"> compoundList[col].append(item[<span class="pl-c1">1</span>])</td>
|
|
|
1758 </tr>
|
|
|
1759 <tr>
|
|
|
1760 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
|
|
|
1761 <td id="LC252" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> i <span class="pl-k">+</span> <span class="pl-c1">1</span></td>
|
|
|
1762 </tr>
|
|
|
1763 <tr>
|
|
|
1764 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
|
|
|
1765 <td id="LC253" class="blob-code blob-code-inner js-file-line"> colormap <span class="pl-k">=</span> plt.cm.tab20 <span class="pl-c"><span class="pl-c">#</span> nipy_spectral, Set1,Paired</span></td>
|
|
|
1766 </tr>
|
|
|
1767 <tr>
|
|
|
1768 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
|
|
|
1769 <td id="LC254" class="blob-code blob-code-inner js-file-line"> cols <span class="pl-k">=</span> [colormap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> np.linspace(<span class="pl-c1">0</span>, <span class="pl-c1">1</span>, <span class="pl-c1">20</span>)]</td>
|
|
|
1770 </tr>
|
|
|
1771 <tr>
|
|
|
1772 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
|
|
|
1773 <td id="LC255" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">9</span>, <span class="pl-c1">6</span>))</td>
|
|
|
1774 </tr>
|
|
|
1775 <tr>
|
|
|
1776 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
|
|
|
1777 <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.figure(num=1,figsize=(12, 6))</span></td>
|
|
|
1778 </tr>
|
|
|
1779 <tr>
|
|
|
1780 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
|
|
|
1781 <td id="LC257" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
|
|
|
1782 </tr>
|
|
|
1783 <tr>
|
|
|
1784 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
|
|
|
1785 <td id="LC258" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> d <span class="pl-k">in</span> myCountries:</td>
|
|
|
1786 </tr>
|
|
|
1787 <tr>
|
|
|
1788 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
|
|
|
1789 <td id="LC259" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> compoundList[i]</td>
|
|
|
1790 </tr>
|
|
|
1791 <tr>
|
|
|
1792 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
|
|
|
1793 <td id="LC260" class="blob-code blob-code-inner js-file-line"> b <span class="pl-k">=</span> a[::<span class="pl-c1">2</span>]</td>
|
|
|
1794 </tr>
|
|
|
1795 <tr>
|
|
|
1796 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
|
|
|
1797 <td id="LC261" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> a[<span class="pl-c1">1</span>::<span class="pl-c1">2</span>]</td>
|
|
|
1798 </tr>
|
|
|
1799 <tr>
|
|
|
1800 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
|
|
|
1801 <td id="LC262" class="blob-code blob-code-inner js-file-line"> ax.scatter(b, c, <span class="pl-v">color</span><span class="pl-k">=</span>cols[i], <span class="pl-v">label</span><span class="pl-k">=</span>myCountries[i])</td>
|
|
|
1802 </tr>
|
|
|
1803 <tr>
|
|
|
1804 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
|
|
|
1805 <td id="LC263" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> i <span class="pl-k">+</span> <span class="pl-c1">1</span></td>
|
|
|
1806 </tr>
|
|
|
1807 <tr>
|
|
|
1808 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
|
|
|
1809 <td id="LC264" class="blob-code blob-code-inner js-file-line"> leg <span class="pl-k">=</span> ax.legend( <span class="pl-v">bbox_to_anchor</span><span class="pl-k">=</span>(<span class="pl-c1">1.02</span>,<span class="pl-c1">1.02</span>), <span class="pl-v">loc</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>upper left<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span>move legend out of plot</span></td>
|
|
|
1810 </tr>
|
|
|
1811 <tr>
|
|
|
1812 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
|
|
|
1813 <td id="LC265" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Principal Component Analysis of the Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$. <span class="pl-pds">"</span></span> \</td>
|
|
|
1814 </tr>
|
|
|
1815 <tr>
|
|
|
1816 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
|
|
|
1817 <td id="LC266" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>The plot reflects the<span class="pl-cce">\n</span>relationships amongst the VSG repertoires of each strain. Strains are color-coded <span class="pl-pds">"</span></span> \</td>
|
|
|
1818 </tr>
|
|
|
1819 <tr>
|
|
|
1820 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
|
|
|
1821 <td id="LC267" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>by location of collection according<span class="pl-cce">\n</span>to key. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018).<span class="pl-pds">"</span></span></td>
|
|
|
1822 </tr>
|
|
|
1823 <tr>
|
|
|
1824 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
|
|
|
1825 <td id="LC268" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span><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>
|
|
|
1826 </tr>
|
|
|
1827 <tr>
|
|
|
1828 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
|
|
|
1829 <td id="LC269" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.title(title, ha = "center", va = "bottom",wrap = "True")</span></td>
|
|
|
1830 </tr>
|
|
|
1831 <tr>
|
|
|
1832 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
|
|
|
1833 <td id="LC270" class="blob-code blob-code-inner js-file-line"> tx <span class="pl-k">=</span> ax.text(<span class="pl-k">-</span><span class="pl-c1">0.1</span>, <span class="pl-k">-</span><span class="pl-c1">0.07</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">transform</span><span class="pl-k">=</span>ax.transAxes, <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>
|
|
|
1834 </tr>
|
|
|
1835 <tr>
|
|
|
1836 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
|
|
|
1837 <td id="LC271" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fig.add_axes([0,0.05,1.05,1.05])</span></td>
|
|
|
1838 </tr>
|
|
|
1839 <tr>
|
|
|
1840 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
|
|
|
1841 <td id="LC272" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fig.tight_layout(rect=[0, 0.03, 1, 0.95])</span></td>
|
|
|
1842 </tr>
|
|
|
1843 <tr>
|
|
|
1844 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
|
|
|
1845 <td id="LC273" class="blob-code blob-code-inner js-file-line"> fig.subplots_adjust(<span class="pl-v">bottom</span> <span class="pl-k">=</span> <span class="pl-c1">0.3</span>)</td>
|
|
|
1846 </tr>
|
|
|
1847 <tr>
|
|
|
1848 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
|
|
|
1849 <td id="LC274" class="blob-code blob-code-inner js-file-line">
|
|
|
1850 </td>
|
|
|
1851 </tr>
|
|
|
1852 <tr>
|
|
|
1853 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
|
|
|
1854 <td id="LC275" class="blob-code blob-code-inner js-file-line"> fig.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/vapPCA.png<span class="pl-pds">"</span></span>, <span class="pl-v">bbox_extra_artists</span><span class="pl-k">=</span>(leg,tx), <span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>tight<span class="pl-pds">'</span></span>)</td>
|
|
|
1855 </tr>
|
|
|
1856 <tr>
|
|
|
1857 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
|
|
|
1858 <td id="LC276" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fig.savefig(htmlresource+"/vapPCA.png", bbox_extra_artists=(leg,))</span></td>
|
|
|
1859 </tr>
|
|
|
1860 <tr>
|
|
|
1861 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
|
|
|
1862 <td id="LC277" 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>
|
|
|
1863 </tr>
|
|
|
1864 <tr>
|
|
|
1865 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
|
|
|
1866 <td id="LC278" class="blob-code blob-code-inner js-file-line"> fig.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/vapPCA.pdf<span class="pl-pds">"</span></span>,<span class="pl-v">bbox_extra_artists</span><span class="pl-k">=</span>(leg,tx), <span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>tight<span class="pl-pds">'</span></span>)</td>
|
|
|
1867 </tr>
|
|
|
1868 <tr>
|
|
|
1869 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
|
|
|
1870 <td id="LC279" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>shutil.copyfile("vapPCA.pdf",PCAfn) # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";</span></td>
|
|
|
1871 </tr>
|
|
|
1872 <tr>
|
|
|
1873 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
|
|
|
1874 <td id="LC280" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
|
|
|
1875 </tr>
|
|
|
1876 <tr>
|
|
|
1877 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
|
|
|
1878 <td id="LC281" class="blob-code blob-code-inner js-file-line">
|
|
|
1879 </td>
|
|
|
1880 </tr>
|
|
|
1881 <tr>
|
|
|
1882 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
|
|
|
1883 <td id="LC282" 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">freqList</span>,<span class="pl-smi">devList</span>):</td>
|
|
|
1884 </tr>
|
|
|
1885 <tr>
|
|
|
1886 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
|
|
|
1887 <td id="LC283" 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>
|
|
|
1888 </tr>
|
|
|
1889 <tr>
|
|
|
1890 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
|
|
|
1891 <td id="LC284" 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>
|
|
|
1892 </tr>
|
|
|
1893 <tr>
|
|
|
1894 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
|
|
|
1895 <td id="LC285" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> name</td>
|
|
|
1896 </tr>
|
|
|
1897 <tr>
|
|
|
1898 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
|
|
|
1899 <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><br/>Genomic Analysis</h3><span class="pl-pds">"</span></span></td>
|
|
|
1900 </tr>
|
|
|
1901 <tr>
|
|
|
1902 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
|
|
|
1903 <td id="LC287" 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:23%; margin-right:23%'>Table Legend: Variant Antigen Profiles of <i>Trypanosoma congolense</i> estimated as the phylotype proportion and as the deviation from the mean across the sample cohort.<br><span class="pl-pds">"</span></span> \</td>
|
|
|
1904 </tr>
|
|
|
1905 <tr>
|
|
|
1906 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
|
|
|
1907 <td id="LC288" 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>
|
|
|
1908 </tr>
|
|
|
1909 <tr>
|
|
|
1910 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
|
|
|
1911 <td id="LC289" 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>
|
|
|
1912 </tr>
|
|
|
1913 <tr>
|
|
|
1914 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
|
|
|
1915 <td id="LC290" class="blob-code blob-code-inner js-file-line">
|
|
|
1916 </td>
|
|
|
1917 </tr>
|
|
|
1918 <tr>
|
|
|
1919 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
|
|
|
1920 <td id="LC291" 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>Deviation from Mean</th></tr><span class="pl-pds">"</span></span></td>
|
|
|
1921 </tr>
|
|
|
1922 <tr>
|
|
|
1923 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
|
|
|
1924 <td id="LC292" 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>
|
|
|
1925 </tr>
|
|
|
1926 <tr>
|
|
|
1927 <td id="L293" class="blob-num js-line-number" data-line-number="293"></td>
|
|
|
1928 <td id="LC293" 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>
|
|
|
1929 </tr>
|
|
|
1930 <tr>
|
|
|
1931 <td id="L294" class="blob-num js-line-number" data-line-number="294"></td>
|
|
|
1932 <td id="LC294" 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>
|
|
|
1933 </tr>
|
|
|
1934 <tr>
|
|
|
1935 <td id="L295" class="blob-num js-line-number" data-line-number="295"></td>
|
|
|
1936 <td id="LC295" 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>
|
|
|
1937 </tr>
|
|
|
1938 <tr>
|
|
|
1939 <td id="L296" class="blob-num js-line-number" data-line-number="296"></td>
|
|
|
1940 <td id="LC296" class="blob-code blob-code-inner js-file-line"> d<span class="pl-k">=</span> <span class="pl-c1">format</span>(devList[i],<span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td>
|
|
|
1941 </tr>
|
|
|
1942 <tr>
|
|
|
1943 <td id="L297" class="blob-num js-line-number" data-line-number="297"></td>
|
|
|
1944 <td id="LC297" 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> d <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td></tr><span class="pl-pds">"</span></span></td>
|
|
|
1945 </tr>
|
|
|
1946 <tr>
|
|
|
1947 <td id="L298" class="blob-num js-line-number" data-line-number="298"></td>
|
|
|
1948 <td id="LC298" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>tabString += "<tr><td>phy" + str(i + 1) + "</td><td>" + str(freqList[i]) + "</td><td>" + str(devList[i]) + "</td></tr>"</span></td>
|
|
|
1949 </tr>
|
|
|
1950 <tr>
|
|
|
1951 <td id="L299" class="blob-num js-line-number" data-line-number="299"></td>
|
|
|
1952 <td id="LC299" 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>
|
|
|
1953 </tr>
|
|
|
1954 <tr>
|
|
|
1955 <td id="L300" class="blob-num js-line-number" data-line-number="300"></td>
|
|
|
1956 <td id="LC300" class="blob-code blob-code-inner js-file-line">
|
|
|
1957 </td>
|
|
|
1958 </tr>
|
|
|
1959 <tr>
|
|
|
1960 <td id="L301" class="blob-num js-line-number" data-line-number="301"></td>
|
|
|
1961 <td id="LC301" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>The Variation Heat Map and Dendrogram</h3><p>The absolute phylotype variation in the sample compared to model dataset<span class="pl-c1">.</span></p><span class="pl-pds">"</span></span></td>
|
|
|
1962 </tr>
|
|
|
1963 <tr>
|
|
|
1964 <td id="L302" class="blob-num js-line-number" data-line-number="302"></td>
|
|
|
1965 <td id="LC302" 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 = 'heatmap<span class="pl-c1">.</span>png' alt='Variation Heatmap' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td>
|
|
|
1966 </tr>
|
|
|
1967 <tr>
|
|
|
1968 <td id="L303" class="blob-num js-line-number" data-line-number="303"></td>
|
|
|
1969 <td id="LC303" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
|
|
|
1970 </tr>
|
|
|
1971 <tr>
|
|
|
1972 <td id="L304" class="blob-num js-line-number" data-line-number="304"></td>
|
|
|
1973 <td id="LC304" class="blob-code blob-code-inner js-file-line">
|
|
|
1974 </td>
|
|
|
1975 </tr>
|
|
|
1976 <tr>
|
|
|
1977 <td id="L305" class="blob-num js-line-number" data-line-number="305"></td>
|
|
|
1978 <td id="LC305" 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><br><br><br><h3>The Deviation Heat Map and Dendrogram</h3><p>The phylotype variation expressed as the deviation from your sample mean compared to the model dataset</p><span class="pl-pds">"</span></span></td>
|
|
|
1979 </tr>
|
|
|
1980 <tr>
|
|
|
1981 <td id="L306" class="blob-num js-line-number" data-line-number="306"></td>
|
|
|
1982 <td id="LC306" 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 = 'dheatmap<span class="pl-c1">.</span>png' alt='Deviation Heatmap' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td>
|
|
|
1983 </tr>
|
|
|
1984 <tr>
|
|
|
1985 <td id="L307" class="blob-num js-line-number" data-line-number="307"></td>
|
|
|
1986 <td id="LC307" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
|
|
|
1987 </tr>
|
|
|
1988 <tr>
|
|
|
1989 <td id="L308" class="blob-num js-line-number" data-line-number="308"></td>
|
|
|
1990 <td id="LC308" class="blob-code blob-code-inner js-file-line">
|
|
|
1991 </td>
|
|
|
1992 </tr>
|
|
|
1993 <tr>
|
|
|
1994 <td id="L309" class="blob-num js-line-number" data-line-number="309"></td>
|
|
|
1995 <td id="LC309" 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><br><br><br><h3>The Variation PCA plot</h3><p>PCA analysis corresponding to absolute variation<span class="pl-c1">.</span> Colour coded according to location</p><span class="pl-pds">"</span></span></td>
|
|
|
1996 </tr>
|
|
|
1997 <tr>
|
|
|
1998 <td id="L310" class="blob-num js-line-number" data-line-number="310"></td>
|
|
|
1999 <td id="LC310" 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 = 'vapPCA<span class="pl-c1">.</span>png' alt='PCA Analysis' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td>
|
|
|
2000 </tr>
|
|
|
2001 <tr>
|
|
|
2002 <td id="L311" class="blob-num js-line-number" data-line-number="311"></td>
|
|
|
2003 <td id="LC311" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString <span class="pl-k">+</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span></div></body></html><span class="pl-pds">"</span></span></td>
|
|
|
2004 </tr>
|
|
|
2005 <tr>
|
|
|
2006 <td id="L312" class="blob-num js-line-number" data-line-number="312"></td>
|
|
|
2007 <td id="LC312" class="blob-code blob-code-inner js-file-line">
|
|
|
2008 </td>
|
|
|
2009 </tr>
|
|
|
2010 <tr>
|
|
|
2011 <td id="L313" class="blob-num js-line-number" data-line-number="313"></td>
|
|
|
2012 <td id="LC313" 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>
|
|
|
2013 </tr>
|
|
|
2014 <tr>
|
|
|
2015 <td id="L314" class="blob-num js-line-number" data-line-number="314"></td>
|
|
|
2016 <td id="LC314" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
|
|
|
2017 </tr>
|
|
|
2018 <tr>
|
|
|
2019 <td id="L315" class="blob-num js-line-number" data-line-number="315"></td>
|
|
|
2020 <td id="LC315" class="blob-code blob-code-inner js-file-line">
|
|
|
2021 </td>
|
|
|
2022 </tr>
|
|
|
2023 <tr>
|
|
|
2024 <td id="L316" class="blob-num js-line-number" data-line-number="316"></td>
|
|
|
2025 <td id="LC316" class="blob-code blob-code-inner js-file-line">
|
|
|
2026 </td>
|
|
|
2027 </tr>
|
|
|
2028 <tr>
|
|
|
2029 <td id="L317" class="blob-num js-line-number" data-line-number="317"></td>
|
|
|
2030 <td id="LC317" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">assemble</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
|
|
|
2031 </tr>
|
|
|
2032 <tr>
|
|
|
2033 <td id="L318" class="blob-num js-line-number" data-line-number="318"></td>
|
|
|
2034 <td id="LC318" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10}</span></td>
|
|
|
2035 </tr>
|
|
|
2036 <tr>
|
|
|
2037 <td id="L319" class="blob-num js-line-number" data-line-number="319"></td>
|
|
|
2038 <td id="LC319" class="blob-code blob-code-inner js-file-line"> assembleWithVelvet(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>kmers<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>covcut<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>]])</td>
|
|
|
2039 </tr>
|
|
|
2040 <tr>
|
|
|
2041 <td id="L320" class="blob-num js-line-number" data-line-number="320"></td>
|
|
|
2042 <td id="LC320" class="blob-code blob-code-inner js-file-line"> contigTranslation(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]])</td>
|
|
|
2043 </tr>
|
|
|
2044 <tr>
|
|
|
2045 <td id="L321" class="blob-num js-line-number" data-line-number="321"></td>
|
|
|
2046 <td id="LC321" class="blob-code blob-code-inner js-file-line"> myCountList <span class="pl-k">=</span> HMMerMotifSearch(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]])</td>
|
|
|
2047 </tr>
|
|
|
2048 <tr>
|
|
|
2049 <td id="L322" class="blob-num js-line-number" data-line-number="322"></td>
|
|
|
2050 <td id="LC322" class="blob-code blob-code-inner js-file-line"> myFreqList <span class="pl-k">=</span> relativeFrequencyTable(myCountList, 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>]]) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_relative_frequncy.csv</span></td>
|
|
|
2051 </tr>
|
|
|
2052 <tr>
|
|
|
2053 <td id="L323" class="blob-num js-line-number" data-line-number="323"></td>
|
|
|
2054 <td id="LC323" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,</span></td>
|
|
|
2055 </tr>
|
|
|
2056 <tr>
|
|
|
2057 <td id="L324" class="blob-num js-line-number" data-line-number="324"></td>
|
|
|
2058 <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,</span></td>
|
|
|
2059 </tr>
|
|
|
2060 <tr>
|
|
|
2061 <td id="L325" class="blob-num js-line-number" data-line-number="325"></td>
|
|
|
2062 <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,</span></td>
|
|
|
2063 </tr>
|
|
|
2064 <tr>
|
|
|
2065 <td id="L326" class="blob-num js-line-number" data-line-number="326"></td>
|
|
|
2066 <td id="LC326" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0372233400402414, 0.17102615694165]</span></td>
|
|
|
2067 </tr>
|
|
|
2068 <tr>
|
|
|
2069 <td id="L327" class="blob-num js-line-number" data-line-number="327"></td>
|
|
|
2070 <td id="LC327" class="blob-code blob-code-inner js-file-line">
|
|
|
2071 </td>
|
|
|
2072 </tr>
|
|
|
2073 <tr>
|
|
|
2074 <td id="L328" class="blob-num js-line-number" data-line-number="328"></td>
|
|
|
2075 <td id="LC328" class="blob-code blob-code-inner js-file-line">
|
|
|
2076 </td>
|
|
|
2077 </tr>
|
|
|
2078 <tr>
|
|
|
2079 <td id="L329" class="blob-num js-line-number" data-line-number="329"></td>
|
|
|
2080 <td id="LC329" class="blob-code blob-code-inner js-file-line"> myDevList <span class="pl-k">=</span> getDeviationFromMean(myFreqList, 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>]]) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_deviation_from_mean.csv</span></td>
|
|
|
2081 </tr>
|
|
|
2082 <tr>
|
|
|
2083 <td id="L330" class="blob-num js-line-number" data-line-number="330"></td>
|
|
|
2084 <td id="LC330" class="blob-code blob-code-inner js-file-line"> relativeFrequencyHeatMap(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], myFreqList,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>
|
|
|
2085 </tr>
|
|
|
2086 <tr>
|
|
|
2087 <td id="L331" class="blob-num js-line-number" data-line-number="331"></td>
|
|
|
2088 <td id="LC331" class="blob-code blob-code-inner js-file-line"> deviationFromMeanHeatMap(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], myDevList,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>
|
|
|
2089 </tr>
|
|
|
2090 <tr>
|
|
|
2091 <td id="L332" class="blob-num js-line-number" data-line-number="332"></td>
|
|
|
2092 <td id="LC332" class="blob-code blob-code-inner js-file-line"> plotPCA(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], myFreqList,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>
|
|
|
2093 </tr>
|
|
|
2094 <tr>
|
|
|
2095 <td id="L333" class="blob-num js-line-number" data-line-number="333"></td>
|
|
|
2096 <td id="LC333" 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>]], myFreqList, myDevList) <span class="pl-c"><span class="pl-c">#</span> assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
|
|
|
2097 </tr>
|
|
|
2098 <tr>
|
|
|
2099 <td id="L334" class="blob-num js-line-number" data-line-number="334"></td>
|
|
|
2100 <td id="LC334" class="blob-code blob-code-inner js-file-line">
|
|
|
2101 </td>
|
|
|
2102 </tr>
|
|
|
2103 <tr>
|
|
|
2104 <td id="L335" class="blob-num js-line-number" data-line-number="335"></td>
|
|
|
2105 <td id="LC335" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">contigs</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
|
|
|
2106 </tr>
|
|
|
2107 <tr>
|
|
|
2108 <td id="L336" class="blob-num js-line-number" data-line-number="336"></td>
|
|
|
2109 <td id="LC336" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6}</span></td>
|
|
|
2110 </tr>
|
|
|
2111 <tr>
|
|
|
2112 <td id="L337" class="blob-num js-line-number" data-line-number="337"></td>
|
|
|
2113 <td id="LC337" class="blob-code blob-code-inner js-file-line">
|
|
|
2114 </td>
|
|
|
2115 </tr>
|
|
|
2116 <tr>
|
|
|
2117 <td id="L338" class="blob-num js-line-number" data-line-number="338"></td>
|
|
|
2118 <td id="LC338" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(args[dict[<span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.fa<span class="pl-pds">"</span></span>)</td>
|
|
|
2119 </tr>
|
|
|
2120 <tr>
|
|
|
2121 <td id="L339" class="blob-num js-line-number" data-line-number="339"></td>
|
|
|
2122 <td id="LC339" class="blob-code blob-code-inner js-file-line">
|
|
|
2123 </td>
|
|
|
2124 </tr>
|
|
|
2125 <tr>
|
|
|
2126 <td id="L340" class="blob-num js-line-number" data-line-number="340"></td>
|
|
|
2127 <td id="LC340" class="blob-code blob-code-inner js-file-line"> </td>
|
|
|
2128 </tr>
|
|
|
2129 <tr>
|
|
|
2130 <td id="L341" class="blob-num js-line-number" data-line-number="341"></td>
|
|
|
2131 <td id="LC341" class="blob-code blob-code-inner js-file-line">
|
|
|
2132 </td>
|
|
|
2133 </tr>
|
|
|
2134 <tr>
|
|
|
2135 <td id="L342" class="blob-num js-line-number" data-line-number="342"></td>
|
|
|
2136 <td id="LC342" class="blob-code blob-code-inner js-file-line"> contigTranslation(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]])</td>
|
|
|
2137 </tr>
|
|
|
2138 <tr>
|
|
|
2139 <td id="L343" class="blob-num js-line-number" data-line-number="343"></td>
|
|
|
2140 <td id="LC343" class="blob-code blob-code-inner js-file-line"> myCountList <span class="pl-k">=</span> HMMerMotifSearch(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]])</td>
|
|
|
2141 </tr>
|
|
|
2142 <tr>
|
|
|
2143 <td id="L344" class="blob-num js-line-number" data-line-number="344"></td>
|
|
|
2144 <td id="LC344" class="blob-code blob-code-inner js-file-line"> myFreqList <span class="pl-k">=</span> relativeFrequencyTable(myCountList, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],</td>
|
|
|
2145 </tr>
|
|
|
2146 <tr>
|
|
|
2147 <td id="L345" class="blob-num js-line-number" data-line-number="345"></td>
|
|
|
2148 <td id="LC345" class="blob-code blob-code-inner js-file-line"> args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_relative_frequncy.csv</span></td>
|
|
|
2149 </tr>
|
|
|
2150 <tr>
|
|
|
2151 <td id="L346" class="blob-num js-line-number" data-line-number="346"></td>
|
|
|
2152 <td id="LC346" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,</span></td>
|
|
|
2153 </tr>
|
|
|
2154 <tr>
|
|
|
2155 <td id="L347" class="blob-num js-line-number" data-line-number="347"></td>
|
|
|
2156 <td id="LC347" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,</span></td>
|
|
|
2157 </tr>
|
|
|
2158 <tr>
|
|
|
2159 <td id="L348" class="blob-num js-line-number" data-line-number="348"></td>
|
|
|
2160 <td id="LC348" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,</span></td>
|
|
|
2161 </tr>
|
|
|
2162 <tr>
|
|
|
2163 <td id="L349" class="blob-num js-line-number" data-line-number="349"></td>
|
|
|
2164 <td id="LC349" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0372233400402414, 0.17102615694165]</span></td>
|
|
|
2165 </tr>
|
|
|
2166 <tr>
|
|
|
2167 <td id="L350" class="blob-num js-line-number" data-line-number="350"></td>
|
|
|
2168 <td id="LC350" class="blob-code blob-code-inner js-file-line">
|
|
|
2169 </td>
|
|
|
2170 </tr>
|
|
|
2171 <tr>
|
|
|
2172 <td id="L351" class="blob-num js-line-number" data-line-number="351"></td>
|
|
|
2173 <td id="LC351" class="blob-code blob-code-inner js-file-line">
|
|
|
2174 </td>
|
|
|
2175 </tr>
|
|
|
2176 <tr>
|
|
|
2177 <td id="L352" class="blob-num js-line-number" data-line-number="352"></td>
|
|
|
2178 <td id="LC352" class="blob-code blob-code-inner js-file-line"> myDevList <span class="pl-k">=</span> getDeviationFromMean(myFreqList, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],</td>
|
|
|
2179 </tr>
|
|
|
2180 <tr>
|
|
|
2181 <td id="L353" class="blob-num js-line-number" data-line-number="353"></td>
|
|
|
2182 <td id="LC353" class="blob-code blob-code-inner js-file-line"> args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_deviation_from_mean.csv</span></td>
|
|
|
2183 </tr>
|
|
|
2184 <tr>
|
|
|
2185 <td id="L354" class="blob-num js-line-number" data-line-number="354"></td>
|
|
|
2186 <td id="LC354" class="blob-code blob-code-inner js-file-line"> relativeFrequencyHeatMap(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], myFreqList, 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>
|
|
|
2187 </tr>
|
|
|
2188 <tr>
|
|
|
2189 <td id="L355" class="blob-num js-line-number" data-line-number="355"></td>
|
|
|
2190 <td id="LC355" class="blob-code blob-code-inner js-file-line"> deviationFromMeanHeatMap(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], myDevList, 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>
|
|
|
2191 </tr>
|
|
|
2192 <tr>
|
|
|
2193 <td id="L356" class="blob-num js-line-number" data-line-number="356"></td>
|
|
|
2194 <td id="LC356" class="blob-code blob-code-inner js-file-line"> plotPCA(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], myFreqList, 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>
|
|
|
2195 </tr>
|
|
|
2196 <tr>
|
|
|
2197 <td id="L357" class="blob-num js-line-number" data-line-number="357"></td>
|
|
|
2198 <td id="LC357" 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>]], myFreqList,</td>
|
|
|
2199 </tr>
|
|
|
2200 <tr>
|
|
|
2201 <td id="L358" class="blob-num js-line-number" data-line-number="358"></td>
|
|
|
2202 <td id="LC358" class="blob-code blob-code-inner js-file-line"> myDevList) <span class="pl-c"><span class="pl-c">#</span> assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
|
|
|
2203 </tr>
|
|
|
2204 <tr>
|
|
|
2205 <td id="L359" class="blob-num js-line-number" data-line-number="359"></td>
|
|
|
2206 <td id="LC359" class="blob-code blob-code-inner js-file-line">
|
|
|
2207 </td>
|
|
|
2208 </tr>
|
|
|
2209 <tr>
|
|
|
2210 <td id="L360" class="blob-num js-line-number" data-line-number="360"></td>
|
|
|
2211 <td id="LC360" class="blob-code blob-code-inner js-file-line">
|
|
|
2212 </td>
|
|
|
2213 </tr>
|
|
|
2214 <tr>
|
|
|
2215 <td id="L361" class="blob-num js-line-number" data-line-number="361"></td>
|
|
|
2216 <td id="LC361" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">genomicProcess</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">exportpdf</span>, <span class="pl-smi">forwardFN</span>, <span class="pl-smi">reverseFN</span>, <span class="pl-smi">htmlfile</span>, <span class="pl-smi">htmlresource</span>):</td>
|
|
|
2217 </tr>
|
|
|
2218 <tr>
|
|
|
2219 <td id="L362" class="blob-num js-line-number" data-line-number="362"></td>
|
|
|
2220 <td id="LC362" class="blob-code blob-code-inner js-file-line"> assembleWithVelvet(inputname,forwardFN,reverseFN)</td>
|
|
|
2221 </tr>
|
|
|
2222 <tr>
|
|
|
2223 <td id="L363" class="blob-num js-line-number" data-line-number="363"></td>
|
|
|
2224 <td id="LC363" class="blob-code blob-code-inner js-file-line"> contigTranslation(inputname)</td>
|
|
|
2225 </tr>
|
|
|
2226 <tr>
|
|
|
2227 <td id="L364" class="blob-num js-line-number" data-line-number="364"></td>
|
|
|
2228 <td id="LC364" class="blob-code blob-code-inner js-file-line"> myCountList <span class="pl-k">=</span> HMMerMotifSearch(inputname)</td>
|
|
|
2229 </tr>
|
|
|
2230 <tr>
|
|
|
2231 <td id="L365" class="blob-num js-line-number" data-line-number="365"></td>
|
|
|
2232 <td id="LC365" class="blob-code blob-code-inner js-file-line"> myFreqList <span class="pl-k">=</span> relativeFrequencyTable(myCountList, inputname, htmlresource) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_relative_frequncy.csv</span></td>
|
|
|
2233 </tr>
|
|
|
2234 <tr>
|
|
|
2235 <td id="L366" class="blob-num js-line-number" data-line-number="366"></td>
|
|
|
2236 <td id="LC366" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,</span></td>
|
|
|
2237 </tr>
|
|
|
2238 <tr>
|
|
|
2239 <td id="L367" class="blob-num js-line-number" data-line-number="367"></td>
|
|
|
2240 <td id="LC367" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,</span></td>
|
|
|
2241 </tr>
|
|
|
2242 <tr>
|
|
|
2243 <td id="L368" class="blob-num js-line-number" data-line-number="368"></td>
|
|
|
2244 <td id="LC368" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,</span></td>
|
|
|
2245 </tr>
|
|
|
2246 <tr>
|
|
|
2247 <td id="L369" class="blob-num js-line-number" data-line-number="369"></td>
|
|
|
2248 <td id="LC369" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0372233400402414, 0.17102615694165]</span></td>
|
|
|
2249 </tr>
|
|
|
2250 <tr>
|
|
|
2251 <td id="L370" class="blob-num js-line-number" data-line-number="370"></td>
|
|
|
2252 <td id="LC370" class="blob-code blob-code-inner js-file-line">
|
|
|
2253 </td>
|
|
|
2254 </tr>
|
|
|
2255 <tr>
|
|
|
2256 <td id="L371" class="blob-num js-line-number" data-line-number="371"></td>
|
|
|
2257 <td id="LC371" class="blob-code blob-code-inner js-file-line">
|
|
|
2258 </td>
|
|
|
2259 </tr>
|
|
|
2260 <tr>
|
|
|
2261 <td id="L372" class="blob-num js-line-number" data-line-number="372"></td>
|
|
|
2262 <td id="LC372" class="blob-code blob-code-inner js-file-line"> myDevList <span class="pl-k">=</span> getDeviationFromMean(myFreqList, inputname,htmlresource) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_deviation_from_mean.csv</span></td>
|
|
|
2263 </tr>
|
|
|
2264 <tr>
|
|
|
2265 <td id="L373" class="blob-num js-line-number" data-line-number="373"></td>
|
|
|
2266 <td id="LC373" class="blob-code blob-code-inner js-file-line">
|
|
|
2267 </td>
|
|
|
2268 </tr>
|
|
|
2269 <tr>
|
|
|
2270 <td id="L374" class="blob-num js-line-number" data-line-number="374"></td>
|
|
|
2271 <td id="LC374" class="blob-code blob-code-inner js-file-line"> relativeFrequencyHeatMap(inputname, myFreqList, exportpdf, htmlresource)</td>
|
|
|
2272 </tr>
|
|
|
2273 <tr>
|
|
|
2274 <td id="L375" class="blob-num js-line-number" data-line-number="375"></td>
|
|
|
2275 <td id="LC375" class="blob-code blob-code-inner js-file-line"> deviationFromMeanHeatMap(inputname, myDevList, exportpdf, htmlresource)</td>
|
|
|
2276 </tr>
|
|
|
2277 <tr>
|
|
|
2278 <td id="L376" class="blob-num js-line-number" data-line-number="376"></td>
|
|
|
2279 <td id="LC376" class="blob-code blob-code-inner js-file-line"> plotPCA(inputname, myFreqList, exportpdf, htmlresource)</td>
|
|
|
2280 </tr>
|
|
|
2281 <tr>
|
|
|
2282 <td id="L377" class="blob-num js-line-number" data-line-number="377"></td>
|
|
|
2283 <td id="LC377" class="blob-code blob-code-inner js-file-line"> createHTML(inputname, htmlfile, myFreqList,myDevList) <span class="pl-c"><span class="pl-c">#</span> assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
|
|
|
2284 </tr>
|
|
|
2285 <tr>
|
|
|
2286 <td id="L378" class="blob-num js-line-number" data-line-number="378"></td>
|
|
|
2287 <td id="LC378" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td>
|
|
|
2288 </tr>
|
|
|
2289 <tr>
|
|
|
2290 <td id="L379" class="blob-num js-line-number" data-line-number="379"></td>
|
|
|
2291 <td id="LC379" class="blob-code blob-code-inner js-file-line">
|
|
|
2292 </td>
|
|
|
2293 </tr>
|
|
|
2294 <tr>
|
|
|
2295 <td id="L380" class="blob-num js-line-number" data-line-number="380"></td>
|
|
|
2296 <td id="LC380" class="blob-code blob-code-inner js-file-line">
|
|
|
2297 </td>
|
|
|
2298 </tr>
|
|
|
2299 <tr>
|
|
|
2300 <td id="L381" class="blob-num js-line-number" data-line-number="381"></td>
|
|
|
2301 <td id="LC381" class="blob-code blob-code-inner js-file-line">
|
|
|
2302 </td>
|
|
|
2303 </tr>
|
|
|
2304 <tr>
|
|
|
2305 <td id="L382" class="blob-num js-line-number" data-line-number="382"></td>
|
|
|
2306 <td id="LC382" 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>
|
|
|
2307 </tr>
|
|
|
2308 <tr>
|
|
|
2309 <td id="L383" class="blob-num js-line-number" data-line-number="383"></td>
|
|
|
2310 <td id="LC383" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>contigTranslation('Tcongo')</span></td>
|
|
|
2311 </tr>
|
|
|
2312 <tr>
|
|
|
2313 <td id="L384" class="blob-num js-line-number" data-line-number="384"></td>
|
|
|
2314 <td id="LC384" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>contigTranslation('Test')</span></td>
|
|
|
2315 </tr>
|
|
|
2316 <tr>
|
|
|
2317 <td id="L385" class="blob-num js-line-number" data-line-number="385"></td>
|
|
|
2318 <td id="LC385" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>newHMMerMotifSearch('Test')</span></td>
|
|
|
2319 </tr>
|
|
|
2320 <tr>
|
|
|
2321 <td id="L386" class="blob-num js-line-number" data-line-number="386"></td>
|
|
|
2322 <td id="LC386" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>HMMerMotifSearch('Tcongo')</span></td>
|
|
|
2323 </tr>
|
|
|
2324 <tr>
|
|
|
2325 <td id="L387" class="blob-num js-line-number" data-line-number="387"></td>
|
|
|
2326 <td id="LC387" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>sys.exit()</span></td>
|
|
|
2327 </tr>
|
|
|
2328 <tr>
|
|
|
2329 <td id="L388" class="blob-num js-line-number" data-line-number="388"></td>
|
|
|
2330 <td id="LC388" class="blob-code blob-code-inner js-file-line">
|
|
|
2331 </td>
|
|
|
2332 </tr>
|
|
|
2333 <tr>
|
|
|
2334 <td id="L389" class="blob-num js-line-number" data-line-number="389"></td>
|
|
|
2335 <td id="LC389" class="blob-code blob-code-inner js-file-line">
|
|
|
2336 </td>
|
|
|
2337 </tr>
|
|
|
2338 <tr>
|
|
|
2339 <td id="L390" class="blob-num js-line-number" data-line-number="390"></td>
|
|
|
2340 <td id="LC390" class="blob-code blob-code-inner js-file-line"> myFreqList <span class="pl-k">=</span> [<span class="pl-c1">0.111670020120724</span>, <span class="pl-c1">0.103621730382294</span>, <span class="pl-c1">0.0784708249496982</span>, <span class="pl-c1">0.0110663983903421</span>,</td>
|
|
|
2341 </tr>
|
|
|
2342 <tr>
|
|
|
2343 <td id="L391" class="blob-num js-line-number" data-line-number="391"></td>
|
|
|
2344 <td id="LC391" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.0543259557344064</span>, <span class="pl-c1">0.0563380281690141</span>, <span class="pl-c1">0.0734406438631791</span>, <span class="pl-c1">0.0160965794768612</span>,</td>
|
|
|
2345 </tr>
|
|
|
2346 <tr>
|
|
|
2347 <td id="L392" class="blob-num js-line-number" data-line-number="392"></td>
|
|
|
2348 <td id="LC392" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.0110663983903421</span>, <span class="pl-c1">0.028169014084507</span>, <span class="pl-c1">0.126760563380282</span>, <span class="pl-c1">0.0583501006036217</span>, <span class="pl-c1">0.062374245472837</span>,</td>
|
|
|
2349 </tr>
|
|
|
2350 <tr>
|
|
|
2351 <td id="L393" class="blob-num js-line-number" data-line-number="393"></td>
|
|
|
2352 <td id="LC393" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.0372233400402414</span>, <span class="pl-c1">0.17102615694165</span>]</td>
|
|
|
2353 </tr>
|
|
|
2354 <tr>
|
|
|
2355 <td id="L394" class="blob-num js-line-number" data-line-number="394"></td>
|
|
|
2356 <td id="LC394" class="blob-code blob-code-inner js-file-line"> myDevList <span class="pl-k">=</span> [<span class="pl-c1">0.000790026</span>,<span class="pl-c1">0.0073109</span>,<span class="pl-k">-</span><span class="pl-c1">0.001151769</span>,<span class="pl-k">-</span><span class="pl-c1">0.004502933</span>,<span class="pl-k">-</span><span class="pl-c1">0.013687421</span>,<span class="pl-k">-</span><span class="pl-c1">0.016159773</span>,<span class="pl-c1">0.021689891</span>,</td>
|
|
|
2357 </tr>
|
|
|
2358 <tr>
|
|
|
2359 <td id="L395" class="blob-num js-line-number" data-line-number="395"></td>
|
|
|
2360 <td id="LC395" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.007863809</span>,<span class="pl-k">-</span><span class="pl-c1">0.003133585</span>,<span class="pl-k">-</span><span class="pl-c1">0.001111709</span>,<span class="pl-k">-</span><span class="pl-c1">0.01313879</span>,<span class="pl-c1">0.0036997</span>,<span class="pl-k">-</span><span class="pl-c1">0.00935284</span>,<span class="pl-c1">0.005640693</span>,<span class="pl-c1">0.015243802</span>]</td>
|
|
|
2361 </tr>
|
|
|
2362 <tr>
|
|
|
2363 <td id="L396" class="blob-num js-line-number" data-line-number="396"></td>
|
|
|
2364 <td id="LC396" class="blob-code blob-code-inner js-file-line">
|
|
|
2365 </td>
|
|
|
2366 </tr>
|
|
|
2367 <tr>
|
|
|
2368 <td id="L397" class="blob-num js-line-number" data-line-number="397"></td>
|
|
|
2369 <td id="LC397" class="blob-code blob-code-inner js-file-line"> relativeFrequencyHeatMap(<span class="pl-s"><span class="pl-pds">'</span>test<span class="pl-pds">'</span></span>, myFreqList, <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>
|
|
|
2370 </tr>
|
|
|
2371 <tr>
|
|
|
2372 <td id="L398" class="blob-num js-line-number" data-line-number="398"></td>
|
|
|
2373 <td id="LC398" class="blob-code blob-code-inner js-file-line"> deviationFromMeanHeatMap(<span class="pl-s"><span class="pl-pds">'</span>test<span class="pl-pds">'</span></span>, myDevList, <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>
|
|
|
2374 </tr>
|
|
|
2375 <tr>
|
|
|
2376 <td id="L399" class="blob-num js-line-number" data-line-number="399"></td>
|
|
|
2377 <td id="LC399" class="blob-code blob-code-inner js-file-line"> plotPCA(<span class="pl-s"><span class="pl-pds">'</span>test<span class="pl-pds">'</span></span>,myFreqList,<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>
|
|
|
2378 </tr>
|
|
|
2379 <tr>
|
|
|
2380 <td id="L400" class="blob-num js-line-number" data-line-number="400"></td>
|
|
|
2381 <td id="LC400" class="blob-code blob-code-inner js-file-line">
|
|
|
2382 </td>
|
|
|
2383 </tr>
|
|
|
2384 <tr>
|
|
|
2385 <td id="L401" class="blob-num js-line-number" data-line-number="401"></td>
|
|
|
2386 <td id="LC401" class="blob-code blob-code-inner js-file-line"> createHTML(<span class="pl-s"><span class="pl-pds">'</span>test<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">"</span>results/test.html<span class="pl-pds">"</span></span>, myFreqList, myDevList)</td>
|
|
|
2387 </tr>
|
|
|
2388 <tr>
|
|
|
2389 <td id="L402" class="blob-num js-line-number" data-line-number="402"></td>
|
|
|
2390 <td id="LC402" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>contigTranslation("Test")</span></td>
|
|
|
2391 </tr>
|
|
|
2392 <tr>
|
|
|
2393 <td id="L403" class="blob-num js-line-number" data-line-number="403"></td>
|
|
|
2394 <td id="LC403" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>myCountList = HMMerMotifSearch("Test")</span></td>
|
|
|
2395 </tr>
|
|
|
2396 <tr>
|
|
|
2397 <td id="L404" class="blob-num js-line-number" data-line-number="404"></td>
|
|
|
2398 <td id="LC404" class="blob-code blob-code-inner js-file-line">
|
|
|
2399 </td>
|
|
|
2400 </tr>
|
|
|
2401 <tr>
|
|
|
2402 <td id="L405" class="blob-num js-line-number" data-line-number="405"></td>
|
|
|
2403 <td id="LC405" class="blob-code blob-code-inner js-file-line">
|
|
|
2404 </td>
|
|
|
2405 </tr>
|
|
|
2406 <tr>
|
|
|
2407 <td id="L406" class="blob-num js-line-number" data-line-number="406"></td>
|
|
|
2408 <td id="LC406" class="blob-code blob-code-inner js-file-line"> sys.exit()</td>
|
|
|
2409 </tr>
|
|
|
2410 </table>
|
|
|
2411
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2412 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
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2413 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar">
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2414 <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg>
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2415 </summary>
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|
2416 <details-menu>
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2417 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
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2418 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li>
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2419 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li>
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2420 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/johnheap/VAPPER-Galaxy/blame/a4e16d71fe985f389930c02f94354b87d3aabadb/Tryp_G.py">View git blame</a></li>
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2421 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li>
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2422 </ul>
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2423 </details-menu>
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2424 </details>
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2425
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2426 </div>
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2427
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2428 </div>
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2429
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2430
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2431
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2432 <details class="details-reset details-overlay details-overlay-dark">
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2433 <summary data-hotkey="l" aria-label="Jump to line"></summary>
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2434 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
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2435 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" />
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2436 <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus>
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2437 <button type="submit" class="btn" data-close-dialog>Go</button>
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2438 </form> </details-dialog>
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2439 </details>
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2440
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2441
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2442
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2443 </div>
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2444 <div class="modal-backdrop js-touch-events"></div>
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2445 </div>
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2446
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2447 </main>
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2448 </div>
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2449
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2450
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2451 </div>
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2452
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2453
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2454 <div class="footer container-lg width-full p-responsive" role="contentinfo">
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2455 <div class="position-relative d-flex flex-row-reverse flex-lg-row flex-wrap flex-lg-nowrap flex-justify-center flex-lg-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light ">
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2456 <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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2457 <li class="mr-3 mr-lg-0">© 2019 <span title="0.91244s from unicorn-7478f9985c-zn698">GitHub</span>, Inc.</li>
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2460 <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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2461 <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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2462 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
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2463 </ul>
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2464
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2465 <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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2466 <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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2467 </a>
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2468 <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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2469 <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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2470 <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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2471 <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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2475
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2476 </ul>
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2477 </div>
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2478 <div class="d-flex flex-justify-center pb-6">
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2479 <span class="f6 text-gray-light"></span>
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2480 </div>
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2481 </div>
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2482
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2483
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2484
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2485 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
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2486 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
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2487 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
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2488 <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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2489 </button>
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2490 You can’t perform that action at this time.
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2491 </div>
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2492
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2493
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2494 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
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2495 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
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2496
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2497 <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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2498
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2499
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2500
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2501 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
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2502 >
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|
2503 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
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2504 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
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2505 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
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2506 </div>
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2507 <template id="site-details-dialog">
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2508 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
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|
2509 <summary role="button" aria-label="Close dialog"></summary>
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|
2510 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
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2511 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
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2512 <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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2513 </button>
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2514 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
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2515 </details-dialog>
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2516 </details>
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2517 </template>
|
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2518
|
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|
2519 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
|
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|
2520 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
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2521 </div>
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2522 </div>
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2523
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2524 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
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2525
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|
2526 </body>
|
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2527 </html>
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2528
|
