Mercurial > repos > johnheap > vapper
changeset 9:a0d5e1f5bec0 draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 14:09:49 -0400 |
| parents | e75a85590041 |
| children | 6450a72e8f6b |
| files | Tryp_V_T.py |
| diffstat | 1 files changed, 2611 insertions(+), 0 deletions(-) [+] |
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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="✓" /> + <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"> + <input type="text" + 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" + data-hotkey="s,/" + name="q" + value="" + placeholder="Search" + data-unscoped-placeholder="Search GitHub" + data-scoped-placeholder="Search" + autocapitalize="off" + aria-autocomplete="list" + aria-controls="jump-to-results" + aria-label="Search" + data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=OeWfhCkNlueqmf+vlMZUOIoZL/xaxMnWSzEKmM+a3P/55zFIrfSMdNtX4Lcjm/pZKDqzddz2DGdPMz+4X5/nxg==" + spellcheck="false" + autocomplete="off" + > + <input type="hidden" class="js-site-search-type-field" name="type" > + <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> + + <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> + +<ul class="d-none js-jump-to-suggestions-template-container"> + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> + <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=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <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> + <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> + <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> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <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"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <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"> + Jump to 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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> + <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> + <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> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <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"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 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width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <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"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <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"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + +</ul> + + </div> + </label> +</form> </div> +</div> + + </div> + + <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"A691:31FC:5350A:9C70E:5CF5626C","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="337eab5a1a33edba9a56afe56b6817bbe2bfb8bfab94836352641826ce53b626" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FTryp_V_T.py"> + Sign in +</a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header 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class="pl-s">* Galaxy Version</span></td> + </tr> + <tr> + <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> + <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2019 University of Liverpool</span></td> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author John Heap, Computational Biology Facility, UoL</span></td> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Silva Pereira, Institute of Infection and Global Health, UoL</span></td> + </tr> + <tr> + <td id="L7" 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class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> + </tr> + <tr> + <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> + <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td> + </tr> + <tr> + <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> + <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> + </tr> + <tr> + <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> + <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td> + </tr> + <tr> + <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> + <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td> + </tr> + <tr> + <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> + <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td> + </tr> + <tr> + <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> + <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td> + </tr> + <tr> + <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> + <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td> + </tr> + <tr> + <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> + <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> + </tr> + <tr> + <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> + <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td> + </tr> + <tr> + <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> + <td id="LC21" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> + <td id="LC22" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> + <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td> + </tr> + <tr> + <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> + <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td> + </tr> + <tr> + <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> + <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td> + </tr> + <tr> + <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> + <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td> + </tr> + <tr> + <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> + <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td> + </tr> + <tr> + <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> + <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td> + </tr> + <tr> + <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> + <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> import matplotlib as mpl</span></td> + </tr> + <tr> + <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> + <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> mpl.use('Agg')</span></td> + </tr> + <tr> + <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> + <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td> + </tr> + <tr> + <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> + <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> numpy <span class="pl-k">as</span> np</td> + </tr> + <tr> + <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> + <td id="LC33" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> + <td id="LC34" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> + <td id="LC35" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> + <td id="LC36" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> + <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> copies the user provided Fasta file to data/reference/file/file.fasta</span></td> + </tr> + <tr> + <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> + <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">uploadUserReferenceFastq</span>(<span class="pl-smi">refFastq</span>):</td> + </tr> + <tr> + <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> + <td id="LC39" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> + </tr> + <tr> + <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> + <td id="LC40" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> 'mydata/test.fasta' -> 'test'</span></td> + </tr> + <tr> + <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> + <td id="LC41" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td> + </tr> + <tr> + <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> + <td id="LC42" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-c"><span class="pl-c">#</span>propose putting file in '/data/reference/ref/</span></td> + </tr> + <tr> + <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> + <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-k">not</span> os.path.isdir(refDir): <span class="pl-c"><span class="pl-c">#</span> if directory data/Reference/ref doesn't exist</span></td> + </tr> + <tr> + <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> + <td id="LC44" class="blob-code blob-code-inner js-file-line"> os.mkdir(refDir)</td> + </tr> + <tr> + <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> + <td id="LC45" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> refDir<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> + <td id="LC46" class="blob-code blob-code-inner js-file-line"> shutil.copy(refFastq, refPath <span class="pl-k">+</span> refBase) <span class="pl-c"><span class="pl-c">#</span>copy reference file into the directory</span></td> + </tr> + <tr> + <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> + <td id="LC47" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2-build <span class="pl-pds">"</span></span> <span class="pl-k">+</span> refPath <span class="pl-k">+</span> refBase<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span><span class="pl-k">+</span>refPath<span class="pl-k">+</span>ref</td> + </tr> + <tr> + <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> + <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>Building the bowtie2 reference files.<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> + <td id="LC49" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> + <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> + </tr> + <tr> + <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> + <td id="LC51" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> + <td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptMapping</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">refFastq</span>, <span class="pl-smi">forwardFN</span>, <span class="pl-smi">reverseFN</span>):</td> + </tr> + <tr> + <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> + <td id="LC53" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> where is our Reference data?</span></td> + </tr> + <tr> + <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> + <td id="LC54" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> + </tr> + <tr> + <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> + <td id="LC55" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>]</td> + </tr> + <tr> + <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> + <td id="LC56" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> + </tr> + <tr> + <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> + <td id="LC57" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> + <td id="LC58" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> refDir <span class="pl-k">+</span> ref</td> + </tr> + <tr> + <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> + <td id="LC59" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> now have reference file so we can proceed with the transcript mapping via bowtie2</span></td> + </tr> + <tr> + <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> + <td id="LC60" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2 -x <span class="pl-pds">"</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -1 <span class="pl-pds">"</span></span><span class="pl-k">+</span>forwardFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -2 <span class="pl-pds">"</span></span><span class="pl-k">+</span>reverseFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -S <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> + <td id="LC61" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> + </tr> + <tr> + <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> + <td id="LC62" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>) <span class="pl-c"><span class="pl-c">#</span>outputs a name.sam file</span></td> + </tr> + <tr> + <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> + <td id="LC63" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> + </tr> + <tr> + <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> + <td id="LC64" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> + <td id="LC65" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> + <td id="LC66" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> + <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">processSamFiles</span>(<span class="pl-smi">inputname</span>):</td> + </tr> + <tr> + <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> + <td id="LC68" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td> + </tr> + <tr> + <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> + <td id="LC69" class="blob-code blob-code-inner js-file-line"> samName <span class="pl-k">=</span> cur_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname</td> + </tr> + <tr> + <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> + <td id="LC70" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools view -bS <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam > <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> + <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> + </tr> + <tr> + <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> + <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> + </tr> + <tr> + <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> + <td id="LC73" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> + <td id="LC74" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools sort <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> + <td id="LC75" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>argstring = <span class="pl-pds">"</span></span><span class="pl-k">+</span>argString)</td> + </tr> + <tr> + <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> + <td id="LC76" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> + <td id="LC77" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> + <td id="LC78" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools index <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> + <td id="LC79" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>argstring = <span class="pl-pds">"</span></span> <span class="pl-k">+</span> argString)</td> + </tr> + <tr> + <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> + <td id="LC80" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> + <td id="LC81" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c"><span class="pl-c">#</span>we have saved out the relevent name.bam, name.sorted and name.sorted.bai files</span></td> + </tr> + <tr> + <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> + <td id="LC82" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> + <td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> we will not have the .gtf file so call cufflinks without -G option</span></td> + </tr> + <tr> + <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> + <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptAbundance</span>(<span class="pl-smi">inputname</span>):</td> + </tr> + <tr> + <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> + <td id="LC85" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>cufflinks -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.cuff -u -p 8 <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> + <td id="LC86" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> + <td id="LC87" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span>remove name.sorted</span></td> + </tr> + <tr> + <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> + <td id="LC88" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> + <td id="LC89" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> + <td id="LC90" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> + </tr> + <tr> + <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> + <td id="LC91" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> + <td id="LC92" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptsForBlast</span>(<span class="pl-smi">name</span>, <span class="pl-smi">refFastq</span>):</td> + </tr> + <tr> + <td id="L93" class="blob-num js-line-number" data-line-number="93"></td> + <td id="LC93" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> quick and dirty just to see.</span></td> + </tr> + <tr> + <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> + <td id="LC94" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> + </tr> + <tr> + <td id="L95" class="blob-num js-line-number" data-line-number="95"></td> + <td id="LC95" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> 'mydata/test.fasta' -> 'test'</span></td> + </tr> + <tr> + <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> + <td id="LC96" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td> + </tr> + <tr> + <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> + <td id="LC97" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> refBase <span class="pl-c"><span class="pl-c">#</span> eg refPath = data/Reference/Trinity/Trinity.fasta</span></td> + </tr> + <tr> + <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> + <td id="LC98" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> used for dirty # refPath = 'Trinity.fasta' # dirty one</span></td> + </tr> + <tr> + <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> + <td id="LC99" class="blob-code blob-code-inner js-file-line"> track_df <span class="pl-k">=</span> pd.read_csv(name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>.cuff/genes.fpkm_tracking<span class="pl-pds">'</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> + <td id="LC100" class="blob-code blob-code-inner js-file-line"> names <span class="pl-k">=</span> track_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> + <td id="LC101" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(len(names))</span></td> + </tr> + <tr> + <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> + <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(names[:5])</span></td> + </tr> + <tr> + <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> + <td id="LC103" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> + <td id="LC104" class="blob-code blob-code-inner js-file-line"> nlist <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> + <td id="LC105" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(names)):</td> + </tr> + <tr> + <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> + <td id="LC106" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> names[n].find(<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> + <td id="LC107" class="blob-code blob-code-inner js-file-line"> nlist.append(names[n][:i])</td> + </tr> + <tr> + <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> + <td id="LC108" class="blob-code blob-code-inner js-file-line"> nameset <span class="pl-k">=</span> <span class="pl-c1">set</span>(nlist) <span class="pl-c"><span class="pl-c">#</span>get unique.</span></td> + </tr> + <tr> + <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> + <td id="LC109" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(refPath, <span class="pl-s"><span class="pl-pds">'</span>r<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> myRef:</td> + </tr> + <tr> + <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> + <td id="LC110" class="blob-code blob-code-inner js-file-line"> refData <span class="pl-k">=</span> myRef.read()</td> + </tr> + <tr> + <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> + <td id="LC111" class="blob-code blob-code-inner js-file-line"> refData<span class="pl-k">=</span> refData<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n</span>><span class="pl-pds">'</span></span></td> + </tr> + <tr> + <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> + <td id="LC112" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> + <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">'</span>_for_blast.fa<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> outfile:</td> + </tr> + <tr> + <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> + <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> trans_id <span class="pl-k">in</span> nameset:</td> + </tr> + <tr> + <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> + <td id="LC115" class="blob-code blob-code-inner js-file-line"> namepos <span class="pl-k">=</span> refData.find(trans_id)</td> + </tr> + <tr> + <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> + <td id="LC116" class="blob-code blob-code-inner js-file-line"> endpos <span class="pl-k">=</span> refData.find(<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>, namepos)</td> + </tr> + <tr> + <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> + <td id="LC117" class="blob-code blob-code-inner js-file-line"> outfile.write(<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span><span class="pl-k">+</span>refData[namepos:endpos])</td> + </tr> + <tr> + <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> + <td id="LC118" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> + <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> + </tr> + <tr> + <td id="L120" class="blob-num js-line-number" data-line-number="120"></td> + <td id="LC120" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> + <td id="LC121" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">html_resource</span>, <span class="pl-smi">database</span>):</td> + </tr> + <tr> + <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> + <td id="LC122" class="blob-code blob-code-inner js-file-line"> db_path <span class="pl-k">=</span> database</td> + </tr> + <tr> + <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> + <td id="LC123" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>blastx -db <span class="pl-pds">"</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -query <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_for_blast.fa -outfmt 10 -out <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> + <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> + </tr> + <tr> + <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> + <td id="LC125" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> + <td id="LC126" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> + </tr> + <tr> + <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> + <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in blastall<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> + <td id="LC128" class="blob-code blob-code-inner js-file-line"> blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> + <td id="LC129" class="blob-code blob-code-inner js-file-line"> blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>mismatch<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>gapopen<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qend<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>sstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>send<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> + <td id="LC130" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]<span class="pl-k">>=</span><span class="pl-c1">70</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">100</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>] <span class="pl-k"><=</span><span class="pl-c1">0.001</span>) ]</td> + </tr> + <tr> + <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> + <td id="LC131" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]] <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td> + </tr> + <tr> + <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> + <td id="LC132" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> need to allocate the transcripts (if allocated more than once to the phylotype with least error.</span></td> + </tr> + <tr> + <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> + <td id="LC133" class="blob-code blob-code-inner js-file-line"> transcripts <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> + <td id="LC134" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> + <td id="LC135" class="blob-code blob-code-inner js-file-line"> transSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(transcripts)</td> + </tr> + <tr> + <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> + <td id="LC136" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> t <span class="pl-k">in</span> transSet:</td> + </tr> + <tr> + <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> + <td id="LC137" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> blastResult_df[(blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> t)]</td> + </tr> + <tr> + <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> + <td id="LC138" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get one with smallest error value</span></td> + </tr> + <tr> + <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> + <td id="LC139" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(t + ":")</span></td> + </tr> + <tr> + <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> + <td id="LC140" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(temp_df)</span></td> + </tr> + <tr> + <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> + <td id="LC141" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> temp_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> + <td id="LC142" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> b_df.append(temp_df.iloc[[<span class="pl-c1">0</span>]])</td> + </tr> + <tr> + <td id="L143" class="blob-num js-line-number" data-line-number="143"></td> + <td id="LC143" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L144" class="blob-num js-line-number" data-line-number="144"></td> + <td id="LC144" class="blob-code blob-code-inner js-file-line"> b_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L145" class="blob-num js-line-number" data-line-number="145"></td> + <td id="LC145" class="blob-code blob-code-inner js-file-line"> b_df.to_csv(test_name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">'</span>_transcript.csv<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L146" class="blob-num js-line-number" data-line-number="146"></td> + <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> b_df</td> + </tr> + <tr> + <td id="L147" class="blob-num js-line-number" data-line-number="147"></td> + <td id="LC147" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L148" class="blob-num js-line-number" data-line-number="148"></td> + <td id="LC148" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L149" class="blob-num js-line-number" data-line-number="149"></td> + <td id="LC149" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createMultiHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">composite_df</span>):</td> + </tr> + <tr> + <td id="L150" class="blob-num js-line-number" data-line-number="150"></td> + <td id="LC150" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td> + </tr> + <tr> + <td id="L151" class="blob-num js-line-number" data-line-number="151"></td> + <td id="LC151" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span></title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L152" class="blob-num js-line-number" data-line-number="152"></td> + <td id="LC152" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Sample name: <span class="pl-pds">"</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L153" class="blob-num js-line-number" data-line-number="153"></td> + <td id="LC153" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L154" class="blob-num js-line-number" data-line-number="154"></td> + <td id="LC154" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Legend: <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L155" class="blob-num js-line-number" data-line-number="155"></td> + <td id="LC155" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptomes. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L156" class="blob-num js-line-number" data-line-number="156"></td> + <td id="LC156" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L157" class="blob-num js-line-number" data-line-number="157"></td> + <td id="LC157" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L158" class="blob-num js-line-number" data-line-number="158"></td> + <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L159" class="blob-num js-line-number" data-line-number="159"></td> + <td id="LC159" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>(Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L160" class="blob-num js-line-number" data-line-number="160"></td> + <td id="LC160" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L161" class="blob-num js-line-number" data-line-number="161"></td> + <td id="LC161" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L162" class="blob-num js-line-number" data-line-number="162"></td> + <td id="LC162" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L163" class="blob-num js-line-number" data-line-number="163"></td> + <td id="LC163" class="blob-code blob-code-inner js-file-line"> wLists <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L164" class="blob-num js-line-number" data-line-number="164"></td> + <td id="LC164" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L165" class="blob-num js-line-number" data-line-number="165"></td> + <td id="LC165" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>,<span class="pl-c1">len</span>(labelList)):</td> + </tr> + <tr> + <td id="L166" class="blob-num js-line-number" data-line-number="166"></td> + <td id="LC166" class="blob-code blob-code-inner js-file-line"> wLists.append(composite_df[labelList[j]])</td> + </tr> + <tr> + <td id="L167" class="blob-num js-line-number" data-line-number="167"></td> + <td id="LC167" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><th><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(labelList[j]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></th><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L168" class="blob-num js-line-number" data-line-number="168"></td> + <td id="LC168" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L169" class="blob-num js-line-number" data-line-number="169"></td> + <td id="LC169" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">+</span> header</td> + </tr> + <tr> + <td id="L170" class="blob-num js-line-number" data-line-number="170"></td> + <td id="LC170" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L171" class="blob-num js-line-number" data-line-number="171"></td> + <td id="LC171" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> composite_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L172" class="blob-num js-line-number" data-line-number="172"></td> + <td id="LC172" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L173" class="blob-num js-line-number" data-line-number="173"></td> + <td id="LC173" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L174" class="blob-num js-line-number" data-line-number="174"></td> + <td id="LC174" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L175" class="blob-num js-line-number" data-line-number="175"></td> + <td id="LC175" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(composite_df)):</td> + </tr> + <tr> + <td id="L176" class="blob-num js-line-number" data-line-number="176"></td> + <td id="LC176" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phyList[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L177" class="blob-num js-line-number" data-line-number="177"></td> + <td id="LC177" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span>):</td> + </tr> + <tr> + <td id="L178" class="blob-num js-line-number" data-line-number="178"></td> + <td id="LC178" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(j)</span></td> + </tr> + <tr> + <td id="L179" class="blob-num js-line-number" data-line-number="179"></td> + <td id="LC179" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(wLists[j][i], <span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L180" class="blob-num js-line-number" data-line-number="180"></td> + <td id="LC180" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L181" class="blob-num js-line-number" data-line-number="181"></td> + <td id="LC181" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-cce">\n</span><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L182" class="blob-num js-line-number" data-line-number="182"></td> + <td id="LC182" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L183" class="blob-num js-line-number" data-line-number="183"></td> + <td id="LC183" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L184" class="blob-num js-line-number" data-line-number="184"></td> + <td id="LC184" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span></h3><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L185" class="blob-num js-line-number" data-line-number="185"></td> + <td id="LC185" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L186" class="blob-num js-line-number" data-line-number="186"></td> + <td id="LC186" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> + </tr> + <tr> + <td id="L187" class="blob-num js-line-number" data-line-number="187"></td> + <td id="LC187" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L188" class="blob-num js-line-number" data-line-number="188"></td> + <td id="LC188" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td> + </tr> + <tr> + <td id="L189" class="blob-num js-line-number" data-line-number="189"></td> + <td id="LC189" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> + </tr> + <tr> + <td id="L190" class="blob-num js-line-number" data-line-number="190"></td> + <td id="LC190" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L191" class="blob-num js-line-number" data-line-number="191"></td> + <td id="LC191" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L192" class="blob-num js-line-number" data-line-number="192"></td> + <td id="LC192" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">sum_df</span>):</td> + </tr> + <tr> + <td id="L193" class="blob-num js-line-number" data-line-number="193"></td> + <td id="LC193" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td> + </tr> + <tr> + <td id="L194" class="blob-num js-line-number" data-line-number="194"></td> + <td id="LC194" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span></title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L195" class="blob-num js-line-number" data-line-number="195"></td> + <td id="LC195" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Sample name: <span class="pl-pds">"</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L196" class="blob-num js-line-number" data-line-number="196"></td> + <td id="LC196" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L197" class="blob-num js-line-number" data-line-number="197"></td> + <td id="LC197" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Legend: <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L198" class="blob-num js-line-number" data-line-number="198"></td> + <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptome. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L199" class="blob-num js-line-number" data-line-number="199"></td> + <td id="LC199" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L200" class="blob-num js-line-number" data-line-number="200"></td> + <td id="LC200" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L201" class="blob-num js-line-number" data-line-number="201"></td> + <td id="LC201" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L202" class="blob-num js-line-number" data-line-number="202"></td> + <td id="LC202" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>(Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L203" class="blob-num js-line-number" data-line-number="203"></td> + <td id="LC203" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L204" class="blob-num js-line-number" data-line-number="204"></td> + <td id="LC204" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L205" class="blob-num js-line-number" data-line-number="205"></td> + <td id="LC205" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;table-layout: auto; margin-left:25%;text-align:center'><tr><th>Phylotype</th><span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L206" class="blob-num js-line-number" data-line-number="206"></td> + <td id="LC206" class="blob-code blob-code-inner js-file-line"> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><th>Combined FPKM</th><th>Weighted Frequency</th></tr><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L207" class="blob-num js-line-number" data-line-number="207"></td> + <td id="LC207" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L208" class="blob-num js-line-number" data-line-number="208"></td> + <td id="LC208" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></td> + </tr> + <tr> + <td id="L209" class="blob-num js-line-number" data-line-number="209"></td> + <td id="LC209" class="blob-code blob-code-inner js-file-line"> phySeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L210" class="blob-num js-line-number" data-line-number="210"></td> + <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> sacSeries = sum_df['saccver']</span></td> + </tr> + <tr> + <td id="L211" class="blob-num js-line-number" data-line-number="211"></td> + <td id="LC211" class="blob-code blob-code-inner js-file-line"> fSeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L212" class="blob-num js-line-number" data-line-number="212"></td> + <td id="LC212" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> fSeries.sum()</td> + </tr> + <tr> + <td id="L213" class="blob-num js-line-number" data-line-number="213"></td> + <td id="LC213" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print("Total="+str(total))</span></td> + </tr> + <tr> + <td id="L214" class="blob-num js-line-number" data-line-number="214"></td> + <td id="LC214" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum_df)):</td> + </tr> + <tr> + <td id="L215" class="blob-num js-line-number" data-line-number="215"></td> + <td id="LC215" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(phySeries[i])</span></td> + </tr> + <tr> + <td id="L216" class="blob-num js-line-number" data-line-number="216"></td> + <td id="LC216" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i], <span class="pl-s"><span class="pl-pds">'</span>.2f<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L217" class="blob-num js-line-number" data-line-number="217"></td> + <td id="LC217" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i]<span class="pl-k">/</span>total, <span class="pl-s"><span class="pl-pds">'</span>.2f<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L218" class="blob-num js-line-number" data-line-number="218"></td> + <td id="LC218" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L219" class="blob-num js-line-number" data-line-number="219"></td> + <td id="LC219" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>w = format(weightList[i], '.4f')</span></td> + </tr> + <tr> + <td id="L220" class="blob-num js-line-number" data-line-number="220"></td> + <td id="LC220" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L221" class="blob-num js-line-number" data-line-number="221"></td> + <td id="LC221" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phySeries[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(w)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L222" class="blob-num js-line-number" data-line-number="222"></td> + <td id="LC222" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L223" class="blob-num js-line-number" data-line-number="223"></td> + <td id="LC223" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span></h3><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L224" class="blob-num js-line-number" data-line-number="224"></td> + <td id="LC224" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L225" class="blob-num js-line-number" data-line-number="225"></td> + <td id="LC225" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> + </tr> + <tr> + <td id="L226" class="blob-num js-line-number" data-line-number="226"></td> + <td id="LC226" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L227" class="blob-num js-line-number" data-line-number="227"></td> + <td id="LC227" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td> + </tr> + <tr> + <td id="L228" class="blob-num js-line-number" data-line-number="228"></td> + <td id="LC228" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> + </tr> + <tr> + <td id="L229" class="blob-num js-line-number" data-line-number="229"></td> + <td id="LC229" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L230" class="blob-num js-line-number" data-line-number="230"></td> + <td id="LC230" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L231" class="blob-num js-line-number" data-line-number="231"></td> + <td id="LC231" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L232" class="blob-num js-line-number" data-line-number="232"></td> + <td id="LC232" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getPhyloNumber</span>(<span class="pl-smi">sac</span>):</td> + </tr> + <tr> + <td id="L233" class="blob-num js-line-number" data-line-number="233"></td> + <td id="LC233" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> sac.find(<span class="pl-s"><span class="pl-pds">'</span>_<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L234" class="blob-num js-line-number" data-line-number="234"></td> + <td id="LC234" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c1">int</span>(sac[<span class="pl-c1">1</span>:i])</td> + </tr> + <tr> + <td id="L235" class="blob-num js-line-number" data-line-number="235"></td> + <td id="LC235" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L236" class="blob-num js-line-number" data-line-number="236"></td> + <td id="LC236" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">combineFPMK</span>(<span class="pl-smi">tdict</span>):</td> + </tr> + <tr> + <td id="L237" class="blob-num js-line-number" data-line-number="237"></td> + <td id="LC237" class="blob-code blob-code-inner js-file-line"> fpkm_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>.cuff/genes.fpkm_tracking<span class="pl-pds">'</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L238" class="blob-num js-line-number" data-line-number="238"></td> + <td id="LC238" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L239" class="blob-num js-line-number" data-line-number="239"></td> + <td id="LC239" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t')</span></td> + </tr> + <tr> + <td id="L240" class="blob-num js-line-number" data-line-number="240"></td> + <td id="LC240" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td> + </tr> + <tr> + <td id="L241" class="blob-num js-line-number" data-line-number="241"></td> + <td id="LC241" class="blob-code blob-code-inner js-file-line"> fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>].apply(<span class="pl-k">lambda</span> <span class="pl-smi">names</span>: names[:names.find(<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>)])</td> + </tr> + <tr> + <td id="L242" class="blob-num js-line-number" data-line-number="242"></td> + <td id="LC242" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td> + </tr> + <tr> + <td id="L243" class="blob-num js-line-number" data-line-number="243"></td> + <td id="LC243" class="blob-code blob-code-inner js-file-line"> reducedBlast_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>_transcript.csv<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L244" class="blob-num js-line-number" data-line-number="244"></td> + <td id="LC244" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> reducedBlast_df = pd.read_csv('TrinityVT_transcript.csv')</span></td> + </tr> + <tr> + <td id="L245" class="blob-num js-line-number" data-line-number="245"></td> + <td id="LC245" class="blob-code blob-code-inner js-file-line"> saccverSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(reducedBlast_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L246" class="blob-num js-line-number" data-line-number="246"></td> + <td id="LC246" class="blob-code blob-code-inner js-file-line"> saccverList <span class="pl-k">=</span> <span class="pl-c1">list</span>(saccverSet)</td> + </tr> + <tr> + <td id="L247" class="blob-num js-line-number" data-line-number="247"></td> + <td id="LC247" class="blob-code blob-code-inner js-file-line"> saccverList.sort()</td> + </tr> + <tr> + <td id="L248" class="blob-num js-line-number" data-line-number="248"></td> + <td id="LC248" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(saccverList[:5])</span></td> + </tr> + <tr> + <td id="L249" class="blob-num js-line-number" data-line-number="249"></td> + <td id="LC249" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L250" class="blob-num js-line-number" data-line-number="250"></td> + <td id="LC250" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> sv <span class="pl-k">in</span> saccverList:</td> + </tr> + <tr> + <td id="L251" class="blob-num js-line-number" data-line-number="251"></td> + <td id="LC251" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(sv)</span></td> + </tr> + <tr> + <td id="L252" class="blob-num js-line-number" data-line-number="252"></td> + <td id="LC252" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> reducedBlast_df[reducedBlast_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> sv]</td> + </tr> + <tr> + <td id="L253" class="blob-num js-line-number" data-line-number="253"></td> + <td id="LC253" class="blob-code blob-code-inner js-file-line"> qList <span class="pl-k">=</span> <span class="pl-c1">list</span>(temp_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L254" class="blob-num js-line-number" data-line-number="254"></td> + <td id="LC254" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> q <span class="pl-k">in</span> qList:</td> + </tr> + <tr> + <td id="L255" class="blob-num js-line-number" data-line-number="255"></td> + <td id="LC255" class="blob-code blob-code-inner js-file-line"> f_df <span class="pl-k">=</span> fpkm_df[(fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> q)]</td> + </tr> + <tr> + <td id="L256" class="blob-num js-line-number" data-line-number="256"></td> + <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-c1">len</span>(f_df) <span class="pl-k">></span> <span class="pl-c1">1</span>:</td> + </tr> + <tr> + <td id="L257" class="blob-num js-line-number" data-line-number="257"></td> + <td id="LC257" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">'</span>WARNING MULTIPLE FPKM<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L258" class="blob-num js-line-number" data-line-number="258"></td> + <td id="LC258" class="blob-code blob-code-inner js-file-line"> new_fpkm<span class="pl-k">=</span><span class="pl-c1">list</span>(f_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L259" class="blob-num js-line-number" data-line-number="259"></td> + <td id="LC259" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> (new_fpkm[<span class="pl-c1">0</span>])</td> + </tr> + <tr> + <td id="L260" class="blob-num js-line-number" data-line-number="260"></td> + <td id="LC260" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(f)</span></td> + </tr> + <tr> + <td id="L261" class="blob-num js-line-number" data-line-number="261"></td> + <td id="LC261" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> new_df.append({<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>: q, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>: sv, <span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>: f}, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L262" class="blob-num js-line-number" data-line-number="262"></td> + <td id="LC262" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> new_df.groupby(<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum().reset_index()</td> + </tr> + <tr> + <td id="L263" class="blob-num js-line-number" data-line-number="263"></td> + <td id="LC263" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L264" class="blob-num js-line-number" data-line-number="264"></td> + <td id="LC264" class="blob-code blob-code-inner js-file-line"> FPKMsum_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> FPKMsum_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: getPhyloNumber(row[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>]), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> + </tr> + <tr> + <td id="L265" class="blob-num js-line-number" data-line-number="265"></td> + <td id="LC265" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L266" class="blob-num js-line-number" data-line-number="266"></td> + <td id="LC266" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.reset_index(<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L267" class="blob-num js-line-number" data-line-number="267"></td> + <td id="LC267" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L268" class="blob-num js-line-number" data-line-number="268"></td> + <td id="LC268" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum_df)</span></td> + </tr> + <tr> + <td id="L269" class="blob-num js-line-number" data-line-number="269"></td> + <td id="LC269" class="blob-code blob-code-inner js-file-line"> FPKMsum_df.to_csv(<span class="pl-s"><span class="pl-pds">'</span>FPKM_sum.csv<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L270" class="blob-num js-line-number" data-line-number="270"></td> + <td id="LC270" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum_df.groupby(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum().reset_index()</td> + </tr> + <tr> + <td id="L271" class="blob-num js-line-number" data-line-number="271"></td> + <td id="LC271" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum2_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L272" class="blob-num js-line-number" data-line-number="272"></td> + <td id="LC272" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L273" class="blob-num js-line-number" data-line-number="273"></td> + <td id="LC273" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum2_df)</span></td> + </tr> + <tr> + <td id="L274" class="blob-num js-line-number" data-line-number="274"></td> + <td id="LC274" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df.to_csv(<span class="pl-s"><span class="pl-pds">'</span>FPKM_sum2.csv<span class="pl-pds">'</span></span>) <span class="pl-c"><span class="pl-c">#</span> in case more than one entry for a particular phylotype</span></td> + </tr> + <tr> + <td id="L275" class="blob-num js-line-number" data-line-number="275"></td> + <td id="LC275" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> FPKMsum_df, FPKMsum2_df</td> + </tr> + <tr> + <td id="L276" class="blob-num js-line-number" data-line-number="276"></td> + <td id="LC276" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L277" class="blob-num js-line-number" data-line-number="277"></td> + <td id="LC277" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L278" class="blob-num js-line-number" data-line-number="278"></td> + <td id="LC278" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L279" class="blob-num js-line-number" data-line-number="279"></td> + <td id="LC279" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">normalisef</span>(<span class="pl-smi">f</span>,<span class="pl-smi">max</span>):</td> + </tr> + <tr> + <td id="L280" class="blob-num js-line-number" data-line-number="280"></td> + <td id="LC280" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> f<span class="pl-k">/</span><span class="pl-c1">max</span></td> + </tr> + <tr> + <td id="L281" class="blob-num js-line-number" data-line-number="281"></td> + <td id="LC281" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L282" class="blob-num js-line-number" data-line-number="282"></td> + <td id="LC282" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getComposite_sum2</span>(<span class="pl-smi">nameList</span>,<span class="pl-smi">sum2_dfs</span>):</td> + </tr> + <tr> + <td id="L283" class="blob-num js-line-number" data-line-number="283"></td> + <td id="LC283" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> lets get a composite sum2_df from all of the sum2_dfs</span></td> + </tr> + <tr> + <td id="L284" class="blob-num js-line-number" data-line-number="284"></td> + <td id="LC284" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L285" class="blob-num js-line-number" data-line-number="285"></td> + <td id="LC285" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L286" class="blob-num js-line-number" data-line-number="286"></td> + <td id="LC286" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td> + </tr> + <tr> + <td id="L287" class="blob-num js-line-number" data-line-number="287"></td> + <td id="LC287" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum()</td> + </tr> + <tr> + <td id="L288" class="blob-num js-line-number" data-line-number="288"></td> + <td id="LC288" class="blob-code blob-code-inner js-file-line"> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_dfs[i].apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], total), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> + </tr> + <tr> + <td id="L289" class="blob-num js-line-number" data-line-number="289"></td> + <td id="LC289" class="blob-code blob-code-inner js-file-line"> pSeries <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L290" class="blob-num js-line-number" data-line-number="290"></td> + <td id="LC290" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pSeries:</td> + </tr> + <tr> + <td id="L291" class="blob-num js-line-number" data-line-number="291"></td> + <td id="LC291" class="blob-code blob-code-inner js-file-line"> phyList.append(p) <span class="pl-c"><span class="pl-c">#</span> get all the phylotypes in this one</span></td> + </tr> + <tr> + <td id="L292" class="blob-num js-line-number" data-line-number="292"></td> + <td id="LC292" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> <span class="pl-c1">list</span>(<span class="pl-c1">set</span>(phyList))</td> + </tr> + <tr> + <td id="L293" class="blob-num js-line-number" data-line-number="293"></td> + <td id="LC293" class="blob-code blob-code-inner js-file-line"> phyList.sort()</td> + </tr> + <tr> + <td id="L294" class="blob-num js-line-number" data-line-number="294"></td> + <td id="LC294" class="blob-code blob-code-inner js-file-line"> composite_sum2_df <span class="pl-k">=</span> pd.DataFrame(phyList, <span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L295" class="blob-num js-line-number" data-line-number="295"></td> + <td id="LC295" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td> + </tr> + <tr> + <td id="L296" class="blob-num js-line-number" data-line-number="296"></td> + <td id="LC296" class="blob-code blob-code-inner js-file-line"> wList <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L297" class="blob-num js-line-number" data-line-number="297"></td> + <td id="LC297" class="blob-code blob-code-inner js-file-line"> pindf <span class="pl-k">=</span> <span class="pl-c1">list</span>(sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L298" class="blob-num js-line-number" data-line-number="298"></td> + <td id="LC298" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(pindf)</span></td> + </tr> + <tr> + <td id="L299" class="blob-num js-line-number" data-line-number="299"></td> + <td id="LC299" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> phyList:</td> + </tr> + <tr> + <td id="L300" class="blob-num js-line-number" data-line-number="300"></td> + <td id="LC300" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> p <span class="pl-k">in</span> pindf:</td> + </tr> + <tr> + <td id="L301" class="blob-num js-line-number" data-line-number="301"></td> + <td id="LC301" class="blob-code blob-code-inner js-file-line"> df <span class="pl-k">=</span> sum2_dfs[i]</td> + </tr> + <tr> + <td id="L302" class="blob-num js-line-number" data-line-number="302"></td> + <td id="LC302" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> df.loc[df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> p, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>].iloc[<span class="pl-c1">0</span>]</td> + </tr> + <tr> + <td id="L303" class="blob-num js-line-number" data-line-number="303"></td> + <td id="LC303" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> + </tr> + <tr> + <td id="L304" class="blob-num js-line-number" data-line-number="304"></td> + <td id="LC304" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">0</span></td> + </tr> + <tr> + <td id="L305" class="blob-num js-line-number" data-line-number="305"></td> + <td id="LC305" class="blob-code blob-code-inner js-file-line"> wList.append(w)</td> + </tr> + <tr> + <td id="L306" class="blob-num js-line-number" data-line-number="306"></td> + <td id="LC306" class="blob-code blob-code-inner js-file-line"> composite_sum2_df[nameList[i]] <span class="pl-k">=</span> wList</td> + </tr> + <tr> + <td id="L307" class="blob-num js-line-number" data-line-number="307"></td> + <td id="LC307" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(composite_sum2_df)</span></td> + </tr> + <tr> + <td id="L308" class="blob-num js-line-number" data-line-number="308"></td> + <td id="LC308" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>composite_sum2_df.to_csv('composite.csv')</span></td> + </tr> + <tr> + <td id="L309" class="blob-num js-line-number" data-line-number="309"></td> + <td id="LC309" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> composite_sum2_df</td> + </tr> + <tr> + <td id="L310" class="blob-num js-line-number" data-line-number="310"></td> + <td id="LC310" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L311" class="blob-num js-line-number" data-line-number="311"></td> + <td id="LC311" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L312" class="blob-num js-line-number" data-line-number="312"></td> + <td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doMultiBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">composite_df</span>): <span class="pl-c"><span class="pl-c">#</span>array of multiple sum2_dfs</span></td> + </tr> + <tr> + <td id="L313" class="blob-num js-line-number" data-line-number="313"></td> + <td id="LC313" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td> + </tr> + <tr> + <td id="L314" class="blob-num js-line-number" data-line-number="314"></td> + <td id="LC314" class="blob-code blob-code-inner js-file-line"> sampnum <span class="pl-k">=</span> <span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span></td> + </tr> + <tr> + <td id="L315" class="blob-num js-line-number" data-line-number="315"></td> + <td id="LC315" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> need to arrange bars</span></td> + </tr> + <tr> + <td id="L316" class="blob-num js-line-number" data-line-number="316"></td> + <td id="LC316" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> number of phylotype = len(composite_df)</span></td> + </tr> + <tr> + <td id="L317" class="blob-num js-line-number" data-line-number="317"></td> + <td id="LC317" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>number of bars = (len(labelist)-1) +1 for space</span></td> + </tr> + <tr> + <td id="L318" class="blob-num js-line-number" data-line-number="318"></td> + <td id="LC318" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> ytick needs to ne</span></td> + </tr> + <tr> + <td id="L319" class="blob-num js-line-number" data-line-number="319"></td> + <td id="LC319" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L320" class="blob-num js-line-number" data-line-number="320"></td> + <td id="LC320" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab10<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L321" class="blob-num js-line-number" data-line-number="321"></td> + <td id="LC321" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td> + </tr> + <tr> + <td id="L322" class="blob-num js-line-number" data-line-number="322"></td> + <td id="LC322" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptomes. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L323" class="blob-num js-line-number" data-line-number="323"></td> + <td id="LC323" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L324" class="blob-num js-line-number" data-line-number="324"></td> + <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>for combined transcript abundance. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L325" class="blob-num js-line-number" data-line-number="325"></td> + <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L326" class="blob-num js-line-number" data-line-number="326"></td> + <td id="LC326" class="blob-code blob-code-inner js-file-line"> width <span class="pl-k">=</span> <span class="pl-c1">0.6</span></td> + </tr> + <tr> + <td id="L327" class="blob-num js-line-number" data-line-number="327"></td> + <td id="LC327" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> np.arange(width<span class="pl-k">*</span>sampnum<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>))</td> + </tr> + <tr> + <td id="L328" class="blob-num js-line-number" data-line-number="328"></td> + <td id="LC328" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(ind)</span></td> + </tr> + <tr> + <td id="L329" class="blob-num js-line-number" data-line-number="329"></td> + <td id="LC329" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span><span class="pl-c1">0.4</span></td> + </tr> + <tr> + <td id="L330" class="blob-num js-line-number" data-line-number="330"></td> + <td id="LC330" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L331" class="blob-num js-line-number" data-line-number="331"></td> + <td id="LC331" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td> + </tr> + <tr> + <td id="L332" class="blob-num js-line-number" data-line-number="332"></td> + <td id="LC332" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L333" class="blob-num js-line-number" data-line-number="333"></td> + <td id="LC333" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L334" class="blob-num js-line-number" data-line-number="334"></td> + <td id="LC334" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> s <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>, <span class="pl-c1">len</span>(labelList)):</td> + </tr> + <tr> + <td id="L335" class="blob-num js-line-number" data-line-number="335"></td> + <td id="LC335" class="blob-code blob-code-inner js-file-line"> ax.barh(ind, composite_df[labelList[s]], width, <span class="pl-v">color</span><span class="pl-k">=</span>palette[s], <span class="pl-v">label</span><span class="pl-k">=</span>labelList[s])</td> + </tr> + <tr> + <td id="L336" class="blob-num js-line-number" data-line-number="336"></td> + <td id="LC336" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> ind <span class="pl-k">+</span> width</td> + </tr> + <tr> + <td id="L337" class="blob-num js-line-number" data-line-number="337"></td> + <td id="LC337" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L338" class="blob-num js-line-number" data-line-number="338"></td> + <td id="LC338" class="blob-code blob-code-inner js-file-line"> ax.set(<span class="pl-v">yticks</span><span class="pl-k">=</span>np.arange(width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">2</span>)<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>)), <span class="pl-v">yticklabels</span><span class="pl-k">=</span>composite_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span> , ylim=[(len(labelList)-1) * width - 1, len(composite_df)])</span></td> + </tr> + <tr> + <td id="L339" class="blob-num js-line-number" data-line-number="339"></td> + <td id="LC339" class="blob-code blob-code-inner js-file-line"> ax.legend()</td> + </tr> + <tr> + <td id="L340" class="blob-num js-line-number" data-line-number="340"></td> + <td id="LC340" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L341" class="blob-num js-line-number" data-line-number="341"></td> + <td id="LC341" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L342" class="blob-num js-line-number" data-line-number="342"></td> + <td id="LC342" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L343" class="blob-num js-line-number" data-line-number="343"></td> + <td id="LC343" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td> + </tr> + <tr> + <td id="L344" class="blob-num js-line-number" data-line-number="344"></td> + <td id="LC344" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">'</span>Weighted Phylotype Frequency<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L345" class="blob-num js-line-number" data-line-number="345"></td> + <td id="LC345" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L346" class="blob-num js-line-number" data-line-number="346"></td> + <td id="LC346" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va="top", wrap="True")</span></td> + </tr> + <tr> + <td id="L347" class="blob-num js-line-number" data-line-number="347"></td> + <td id="LC347" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td> + </tr> + <tr> + <td id="L348" class="blob-num js-line-number" data-line-number="348"></td> + <td id="LC348" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L349" class="blob-num js-line-number" data-line-number="349"></td> + <td id="LC349" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.92</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td> + </tr> + <tr> + <td id="L350" class="blob-num js-line-number" data-line-number="350"></td> + <td id="LC350" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>True<span class="pl-pds">'</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>left<span class="pl-pds">'</span></span>,)</td> + </tr> + <tr> + <td id="L351" class="blob-num js-line-number" data-line-number="351"></td> + <td id="LC351" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L352" class="blob-num js-line-number" data-line-number="352"></td> + <td id="LC352" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L353" class="blob-num js-line-number" data-line-number="353"></td> + <td id="LC353" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td> + </tr> + <tr> + <td id="L354" class="blob-num js-line-number" data-line-number="354"></td> + <td id="LC354" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>phylotypes.pdf<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L355" class="blob-num js-line-number" data-line-number="355"></td> + <td id="LC355" class="blob-code blob-code-inner js-file-line"> plt.show()</td> + </tr> + <tr> + <td id="L356" class="blob-num js-line-number" data-line-number="356"></td> + <td id="LC356" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> + </tr> + <tr> + <td id="L357" class="blob-num js-line-number" data-line-number="357"></td> + <td id="LC357" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L358" class="blob-num js-line-number" data-line-number="358"></td> + <td id="LC358" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L359" class="blob-num js-line-number" data-line-number="359"></td> + <td id="LC359" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L360" class="blob-num js-line-number" data-line-number="360"></td> + <td id="LC360" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">sum2_df</span>):</td> + </tr> + <tr> + <td id="L361" class="blob-num js-line-number" data-line-number="361"></td> + <td id="LC361" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab20<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L362" class="blob-num js-line-number" data-line-number="362"></td> + <td id="LC362" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td> + </tr> + <tr> + <td id="L363" class="blob-num js-line-number" data-line-number="363"></td> + <td id="LC363" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptome. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L364" class="blob-num js-line-number" data-line-number="364"></td> + <td id="LC364" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L365" class="blob-num js-line-number" data-line-number="365"></td> + <td id="LC365" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>for combined transcript abundance. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L366" class="blob-num js-line-number" data-line-number="366"></td> + <td id="LC366" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L367" class="blob-num js-line-number" data-line-number="367"></td> + <td id="LC367" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get a list of phylotype, create equivalent of saccver, get a list of</span></td> + </tr> + <tr> + <td id="L368" class="blob-num js-line-number" data-line-number="368"></td> + <td id="LC368" class="blob-code blob-code-inner js-file-line"> maxFPKM <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].max()</td> + </tr> + <tr> + <td id="L369" class="blob-num js-line-number" data-line-number="369"></td> + <td id="LC369" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum()</td> + </tr> + <tr> + <td id="L370" class="blob-num js-line-number" data-line-number="370"></td> + <td id="LC370" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L371" class="blob-num js-line-number" data-line-number="371"></td> + <td id="LC371" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Normalised<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], maxFPKM),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> + </tr> + <tr> + <td id="L372" class="blob-num js-line-number" data-line-number="372"></td> + <td id="LC372" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Weighted<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], total),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> + </tr> + <tr> + <td id="L373" class="blob-num js-line-number" data-line-number="373"></td> + <td id="LC373" class="blob-code blob-code-inner js-file-line"> pList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L374" class="blob-num js-line-number" data-line-number="374"></td> + <td id="LC374" class="blob-code blob-code-inner js-file-line"> phList <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L375" class="blob-num js-line-number" data-line-number="375"></td> + <td id="LC375" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pList:</td> + </tr> + <tr> + <td id="L376" class="blob-num js-line-number" data-line-number="376"></td> + <td id="LC376" class="blob-code blob-code-inner js-file-line"> phList.append(<span class="pl-c1">str</span>(p))</td> + </tr> + <tr> + <td id="L377" class="blob-num js-line-number" data-line-number="377"></td> + <td id="LC377" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L378" class="blob-num js-line-number" data-line-number="378"></td> + <td id="LC378" class="blob-code blob-code-inner js-file-line"> fList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Weighted<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L379" class="blob-num js-line-number" data-line-number="379"></td> + <td id="LC379" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(phList)<span class="pl-k">*</span><span class="pl-c1">0.3</span></td> + </tr> + <tr> + <td id="L380" class="blob-num js-line-number" data-line-number="380"></td> + <td id="LC380" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td> + </tr> + <tr> + <td id="L381" class="blob-num js-line-number" data-line-number="381"></td> + <td id="LC381" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L382" class="blob-num js-line-number" data-line-number="382"></td> + <td id="LC382" class="blob-code blob-code-inner js-file-line"> ax.barh(phList, fList, <span class="pl-v">color</span><span class="pl-k">=</span>palette)</td> + </tr> + <tr> + <td id="L383" class="blob-num js-line-number" data-line-number="383"></td> + <td id="LC383" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L384" class="blob-num js-line-number" data-line-number="384"></td> + <td id="LC384" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td> + </tr> + <tr> + <td id="L385" class="blob-num js-line-number" data-line-number="385"></td> + <td id="LC385" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">'</span>Weighted Phylotype Frequency<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L386" class="blob-num js-line-number" data-line-number="386"></td> + <td id="LC386" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L387" class="blob-num js-line-number" data-line-number="387"></td> + <td id="LC387" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va="top", wrap="True")</span></td> + </tr> + <tr> + <td id="L388" class="blob-num js-line-number" data-line-number="388"></td> + <td id="LC388" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td> + </tr> + <tr> + <td id="L389" class="blob-num js-line-number" data-line-number="389"></td> + <td id="LC389" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td> + </tr> + <tr> + <td id="L390" class="blob-num js-line-number" data-line-number="390"></td> + <td id="LC390" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>True<span class="pl-pds">'</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>left<span class="pl-pds">'</span></span>,)</td> + </tr> + <tr> + <td id="L391" class="blob-num js-line-number" data-line-number="391"></td> + <td id="LC391" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L392" class="blob-num js-line-number" data-line-number="392"></td> + <td id="LC392" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L393" class="blob-num js-line-number" data-line-number="393"></td> + <td id="LC393" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td> + </tr> + <tr> + <td id="L394" class="blob-num js-line-number" data-line-number="394"></td> + <td id="LC394" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>phylotypes.pdf<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L395" class="blob-num js-line-number" data-line-number="395"></td> + <td id="LC395" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.show()</span></td> + </tr> + <tr> + <td id="L396" class="blob-num js-line-number" data-line-number="396"></td> + <td id="LC396" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> + </tr> + <tr> + <td id="L397" class="blob-num js-line-number" data-line-number="397"></td> + <td id="LC397" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L398" class="blob-num js-line-number" data-line-number="398"></td> + <td id="LC398" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}</span></td> + </tr> + <tr> + <td id="L399" class="blob-num js-line-number" data-line-number="399"></td> + <td id="LC399" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L400" class="blob-num js-line-number" data-line-number="400"></td> + <td id="LC400" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptomicProcess</span>(<span class="pl-smi">args</span>,<span class="pl-smi">argdict</span>):</td> + </tr> + <tr> + <td id="L401" class="blob-num js-line-number" data-line-number="401"></td> + <td id="LC401" class="blob-code blob-code-inner js-file-line"> tdict <span class="pl-k">=</span> {}</td> + </tr> + <tr> + <td id="L402" class="blob-num js-line-number" data-line-number="402"></td> + <td id="LC402" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]</td> + </tr> + <tr> + <td id="L403" class="blob-num js-line-number" data-line-number="403"></td> + <td id="LC403" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>]]</td> + </tr> + <tr> + <td id="L404" class="blob-num js-line-number" data-line-number="404"></td> + <td id="LC404" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>]]</td> + </tr> + <tr> + <td id="L405" class="blob-num js-line-number" data-line-number="405"></td> + <td id="LC405" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]]</td> + </tr> + <tr> + <td id="L406" class="blob-num js-line-number" data-line-number="406"></td> + <td id="LC406" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>vivax_trans_database<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">'</span></span></td> + </tr> + <tr> + <td id="L407" class="blob-num js-line-number" data-line-number="407"></td> + <td id="LC407" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]]</td> + </tr> + <tr> + <td id="L408" class="blob-num js-line-number" data-line-number="408"></td> + <td id="LC408" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]]</td> + </tr> + <tr> + <td id="L409" class="blob-num js-line-number" data-line-number="409"></td> + <td id="LC409" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]</td> + </tr> + <tr> + <td id="L410" class="blob-num js-line-number" data-line-number="410"></td> + <td id="LC410" class="blob-code blob-code-inner js-file-line"> </td> + </tr> + <tr> + <td id="L411" class="blob-num js-line-number" data-line-number="411"></td> + <td id="LC411" class="blob-code blob-code-inner js-file-line"> uploadUserReferenceFastq(tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L412" class="blob-num js-line-number" data-line-number="412"></td> + <td id="LC412" class="blob-code blob-code-inner js-file-line"> transcriptMapping(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses bowtie</span></td> + </tr> + <tr> + <td id="L413" class="blob-num js-line-number" data-line-number="413"></td> + <td id="LC413" class="blob-code blob-code-inner js-file-line"> processSamFiles(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses samtools</span></td> + </tr> + <tr> + <td id="L414" class="blob-num js-line-number" data-line-number="414"></td> + <td id="LC414" class="blob-code blob-code-inner js-file-line"> transcriptAbundance(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -> ?.cuff/*.*</span></td> + </tr> + <tr> + <td id="L415" class="blob-num js-line-number" data-line-number="415"></td> + <td id="LC415" class="blob-code blob-code-inner js-file-line"> transcriptsForBlast(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>creates name+4blast.fa</span></td> + </tr> + <tr> + <td id="L416" class="blob-num js-line-number" data-line-number="416"></td> + <td id="LC416" class="blob-code blob-code-inner js-file-line"> blastContigs(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">'</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L417" class="blob-num js-line-number" data-line-number="417"></td> + <td id="LC417" class="blob-code blob-code-inner js-file-line"> sum_df, sum2_df <span class="pl-k">=</span> combineFPMK(tdict)</td> + </tr> + <tr> + <td id="L418" class="blob-num js-line-number" data-line-number="418"></td> + <td id="LC418" class="blob-code blob-code-inner js-file-line"> doBarChart(tdict, sum2_df)</td> + </tr> + <tr> + <td id="L419" class="blob-num js-line-number" data-line-number="419"></td> + <td id="LC419" class="blob-code blob-code-inner js-file-line"> createHTML(tdict, sum_df)</td> + </tr> + <tr> + <td id="L420" class="blob-num js-line-number" data-line-number="420"></td> + <td id="LC420" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L421" class="blob-num js-line-number" data-line-number="421"></td> + <td id="LC421" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L422" class="blob-num js-line-number" data-line-number="422"></td> + <td id="LC422" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>__main__<span class="pl-pds">"</span></span>:</td> + </tr> + <tr> + <td id="L423" class="blob-num js-line-number" data-line-number="423"></td> + <td id="LC423" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">exit</span>()</td> + </tr> + <tr> + <td id="L424" class="blob-num js-line-number" data-line-number="424"></td> + <td id="LC424" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L425" class="blob-num js-line-number" data-line-number="425"></td> + <td id="LC425" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> +</table> + + <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true"> + <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar"> + <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> + </summary> + <details-menu> + <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px"> + <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> + <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" 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