Mercurial > repos > johnheap > vapper
comparison Tryp_V_T.py @ 9:a0d5e1f5bec0 draft
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author | johnheap |
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date | Mon, 03 Jun 2019 14:09:49 -0400 |
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children | fe79425b1fa4 |
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249 </details> | |
250 </li> | |
251 </ul> | |
252 </nav> | |
253 | |
254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left"> | |
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256 <div class="header-search flex-self-stretch flex-lg-self-auto mr-0 mr-lg-3 mb-3 mb-lg-0 scoped-search site-scoped-search js-site-search position-relative js-jump-to" | |
257 role="combobox" | |
258 aria-owns="jump-to-results" | |
259 aria-label="Search or jump to" | |
260 aria-haspopup="listbox" | |
261 aria-expanded="false" | |
262 > | |
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265 <label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container"> | |
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278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=OeWfhCkNlueqmf+vlMZUOIoZL/xaxMnWSzEKmM+a3P/55zFIrfSMdNtX4Lcjm/pZKDqzddz2DGdPMz+4X5/nxg==" | |
279 spellcheck="false" | |
280 autocomplete="off" | |
281 > | |
282 <input type="hidden" class="js-site-search-type-field" name="type" > | |
283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> | |
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294 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> | |
295 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> | |
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297 | |
298 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> | |
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301 </div> | |
302 | |
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304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> | |
305 In this repository | |
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308 All GitHub | |
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314 Jump to | |
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326 </ul> | |
327 | |
328 <ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container"> | |
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331 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option"> | |
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338 | |
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370 | |
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372 | |
373 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> | |
374 </div> | |
375 | |
376 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> | |
377 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> | |
378 In this repository | |
379 </span> | |
380 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> | |
381 All GitHub | |
382 </span> | |
383 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> | |
384 </div> | |
385 | |
386 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> | |
387 Jump to | |
388 <span class="d-inline-block ml-1 v-align-middle">↵</span> | |
389 </div> | |
390 </a> | |
391 </li> | |
392 | |
393 | |
394 </ul> | |
395 | |
396 </div> | |
397 </label> | |
398 </form> </div> | |
399 </div> | |
400 | |
401 </div> | |
402 | |
403 <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"> | |
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405 </a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"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="ae884c1f61e6facf2cb96fcd7d55fbcf227cb7989e192de2cb6c5ab5c46e53d1" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo"> | |
406 Sign up | |
407 </a> </div> | |
408 </div> | |
409 </div> | |
410 </header> | |
411 | |
412 </div> | |
413 | |
414 <div id="start-of-content" class="show-on-focus"></div> | |
415 | |
416 | |
417 <div id="js-flash-container"> | |
418 | |
419 </div> | |
420 | |
421 | |
422 | |
423 <div class="application-main " data-commit-hovercards-enabled> | |
424 <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> | |
425 <main > | |
426 | |
427 | |
428 | |
429 | |
430 | |
431 | |
432 | |
433 | |
434 | |
435 | |
436 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav pt-0 pt-lg-4 "> | |
437 <div class="repohead-details-container clearfix container-lg p-responsive d-none d-lg-block"> | |
438 | |
439 <ul class="pagehead-actions"> | |
440 | |
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444 <li> | |
445 | |
446 <a class="tooltipped tooltipped-s btn btn-sm btn-with-count" aria-label="You must be signed in to watch a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"notification subscription menu watch","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="af7329bf60da95c08a620876666a89de6aa2bf96a8da8486f5eb50741ad8743e" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy"> | |
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448 Watch | |
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457 <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to star a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"star button","repository_id":139730674,"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="0db565041ee36ff7a0a3ca6a8ab0c55e0708db9b7f32415674420a32f9615882" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy"> | |
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459 Star | |
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721 <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">"""</span></span></td> | |
722 </tr> | |
723 <tr> | |
724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> | |
725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s">* Galaxy Version</span></td> | |
726 </tr> | |
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729 <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td> | |
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734 </tr> | |
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736 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> | |
737 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author John Heap, Computational Biology Facility, UoL</span></td> | |
738 </tr> | |
739 <tr> | |
740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> | |
741 <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Silva Pereira, Institute of Infection and Global Health, UoL</span></td> | |
742 </tr> | |
743 <tr> | |
744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> | |
745 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> | |
746 </tr> | |
747 <tr> | |
748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> | |
749 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the "License");</span></td> | |
750 </tr> | |
751 <tr> | |
752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> | |
753 <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td> | |
754 </tr> | |
755 <tr> | |
756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> | |
757 <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td> | |
758 </tr> | |
759 <tr> | |
760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> | |
761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> | |
762 </tr> | |
763 <tr> | |
764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> | |
765 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td> | |
766 </tr> | |
767 <tr> | |
768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> | |
769 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> | |
770 </tr> | |
771 <tr> | |
772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> | |
773 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td> | |
774 </tr> | |
775 <tr> | |
776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> | |
777 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td> | |
778 </tr> | |
779 <tr> | |
780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> | |
781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td> | |
782 </tr> | |
783 <tr> | |
784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> | |
785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td> | |
786 </tr> | |
787 <tr> | |
788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> | |
789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td> | |
790 </tr> | |
791 <tr> | |
792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> | |
793 <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> | |
794 </tr> | |
795 <tr> | |
796 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> | |
797 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td> | |
798 </tr> | |
799 <tr> | |
800 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> | |
801 <td id="LC21" class="blob-code blob-code-inner js-file-line"> | |
802 </td> | |
803 </tr> | |
804 <tr> | |
805 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> | |
806 <td id="LC22" class="blob-code blob-code-inner js-file-line"> | |
807 </td> | |
808 </tr> | |
809 <tr> | |
810 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> | |
811 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td> | |
812 </tr> | |
813 <tr> | |
814 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> | |
815 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td> | |
816 </tr> | |
817 <tr> | |
818 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> | |
819 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td> | |
820 </tr> | |
821 <tr> | |
822 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> | |
823 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td> | |
824 </tr> | |
825 <tr> | |
826 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> | |
827 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td> | |
828 </tr> | |
829 <tr> | |
830 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> | |
831 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td> | |
832 </tr> | |
833 <tr> | |
834 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> | |
835 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> import matplotlib as mpl</span></td> | |
836 </tr> | |
837 <tr> | |
838 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> | |
839 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> mpl.use('Agg')</span></td> | |
840 </tr> | |
841 <tr> | |
842 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> | |
843 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td> | |
844 </tr> | |
845 <tr> | |
846 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> | |
847 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> numpy <span class="pl-k">as</span> np</td> | |
848 </tr> | |
849 <tr> | |
850 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> | |
851 <td id="LC33" class="blob-code blob-code-inner js-file-line"> | |
852 </td> | |
853 </tr> | |
854 <tr> | |
855 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> | |
856 <td id="LC34" class="blob-code blob-code-inner js-file-line"> | |
857 </td> | |
858 </tr> | |
859 <tr> | |
860 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> | |
861 <td id="LC35" class="blob-code blob-code-inner js-file-line"> | |
862 </td> | |
863 </tr> | |
864 <tr> | |
865 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> | |
866 <td id="LC36" class="blob-code blob-code-inner js-file-line"> | |
867 </td> | |
868 </tr> | |
869 <tr> | |
870 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> | |
871 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> copies the user provided Fasta file to data/reference/file/file.fasta</span></td> | |
872 </tr> | |
873 <tr> | |
874 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> | |
875 <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">uploadUserReferenceFastq</span>(<span class="pl-smi">refFastq</span>):</td> | |
876 </tr> | |
877 <tr> | |
878 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> | |
879 <td id="LC39" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> | |
880 </tr> | |
881 <tr> | |
882 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> | |
883 <td id="LC40" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> 'mydata/test.fasta' -> 'test'</span></td> | |
884 </tr> | |
885 <tr> | |
886 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> | |
887 <td id="LC41" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td> | |
888 </tr> | |
889 <tr> | |
890 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> | |
891 <td id="LC42" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-c"><span class="pl-c">#</span>propose putting file in '/data/reference/ref/</span></td> | |
892 </tr> | |
893 <tr> | |
894 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> | |
895 <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-k">not</span> os.path.isdir(refDir): <span class="pl-c"><span class="pl-c">#</span> if directory data/Reference/ref doesn't exist</span></td> | |
896 </tr> | |
897 <tr> | |
898 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> | |
899 <td id="LC44" class="blob-code blob-code-inner js-file-line"> os.mkdir(refDir)</td> | |
900 </tr> | |
901 <tr> | |
902 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> | |
903 <td id="LC45" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> refDir<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span></td> | |
904 </tr> | |
905 <tr> | |
906 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> | |
907 <td id="LC46" class="blob-code blob-code-inner js-file-line"> shutil.copy(refFastq, refPath <span class="pl-k">+</span> refBase) <span class="pl-c"><span class="pl-c">#</span>copy reference file into the directory</span></td> | |
908 </tr> | |
909 <tr> | |
910 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> | |
911 <td id="LC47" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2-build <span class="pl-pds">"</span></span> <span class="pl-k">+</span> refPath <span class="pl-k">+</span> refBase<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span><span class="pl-k">+</span>refPath<span class="pl-k">+</span>ref</td> | |
912 </tr> | |
913 <tr> | |
914 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> | |
915 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>Building the bowtie2 reference files.<span class="pl-pds">"</span></span>)</td> | |
916 </tr> | |
917 <tr> | |
918 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> | |
919 <td id="LC49" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
920 </tr> | |
921 <tr> | |
922 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> | |
923 <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> | |
924 </tr> | |
925 <tr> | |
926 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> | |
927 <td id="LC51" class="blob-code blob-code-inner js-file-line"> | |
928 </td> | |
929 </tr> | |
930 <tr> | |
931 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> | |
932 <td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptMapping</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">refFastq</span>, <span class="pl-smi">forwardFN</span>, <span class="pl-smi">reverseFN</span>):</td> | |
933 </tr> | |
934 <tr> | |
935 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> | |
936 <td id="LC53" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> where is our Reference data?</span></td> | |
937 </tr> | |
938 <tr> | |
939 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> | |
940 <td id="LC54" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> | |
941 </tr> | |
942 <tr> | |
943 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> | |
944 <td id="LC55" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>]</td> | |
945 </tr> | |
946 <tr> | |
947 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> | |
948 <td id="LC56" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> | |
949 </tr> | |
950 <tr> | |
951 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> | |
952 <td id="LC57" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span></td> | |
953 </tr> | |
954 <tr> | |
955 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> | |
956 <td id="LC58" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> refDir <span class="pl-k">+</span> ref</td> | |
957 </tr> | |
958 <tr> | |
959 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> | |
960 <td id="LC59" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> now have reference file so we can proceed with the transcript mapping via bowtie2</span></td> | |
961 </tr> | |
962 <tr> | |
963 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> | |
964 <td id="LC60" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2 -x <span class="pl-pds">"</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -1 <span class="pl-pds">"</span></span><span class="pl-k">+</span>forwardFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -2 <span class="pl-pds">"</span></span><span class="pl-k">+</span>reverseFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -S <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam<span class="pl-pds">"</span></span></td> | |
965 </tr> | |
966 <tr> | |
967 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> | |
968 <td id="LC61" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> | |
969 </tr> | |
970 <tr> | |
971 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> | |
972 <td id="LC62" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>) <span class="pl-c"><span class="pl-c">#</span>outputs a name.sam file</span></td> | |
973 </tr> | |
974 <tr> | |
975 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> | |
976 <td id="LC63" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> | |
977 </tr> | |
978 <tr> | |
979 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> | |
980 <td id="LC64" class="blob-code blob-code-inner js-file-line"> | |
981 </td> | |
982 </tr> | |
983 <tr> | |
984 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> | |
985 <td id="LC65" class="blob-code blob-code-inner js-file-line"> | |
986 </td> | |
987 </tr> | |
988 <tr> | |
989 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> | |
990 <td id="LC66" class="blob-code blob-code-inner js-file-line"> | |
991 </td> | |
992 </tr> | |
993 <tr> | |
994 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> | |
995 <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">processSamFiles</span>(<span class="pl-smi">inputname</span>):</td> | |
996 </tr> | |
997 <tr> | |
998 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> | |
999 <td id="LC68" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td> | |
1000 </tr> | |
1001 <tr> | |
1002 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> | |
1003 <td id="LC69" class="blob-code blob-code-inner js-file-line"> samName <span class="pl-k">=</span> cur_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname</td> | |
1004 </tr> | |
1005 <tr> | |
1006 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> | |
1007 <td id="LC70" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools view -bS <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam > <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span></td> | |
1008 </tr> | |
1009 <tr> | |
1010 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> | |
1011 <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> | |
1012 </tr> | |
1013 <tr> | |
1014 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> | |
1015 <td id="LC72" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1016 </tr> | |
1017 <tr> | |
1018 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> | |
1019 <td id="LC73" class="blob-code blob-code-inner js-file-line"> | |
1020 </td> | |
1021 </tr> | |
1022 <tr> | |
1023 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> | |
1024 <td id="LC74" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools sort <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span></td> | |
1025 </tr> | |
1026 <tr> | |
1027 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> | |
1028 <td id="LC75" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>argstring = <span class="pl-pds">"</span></span><span class="pl-k">+</span>argString)</td> | |
1029 </tr> | |
1030 <tr> | |
1031 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> | |
1032 <td id="LC76" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1033 </tr> | |
1034 <tr> | |
1035 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> | |
1036 <td id="LC77" class="blob-code blob-code-inner js-file-line"> | |
1037 </td> | |
1038 </tr> | |
1039 <tr> | |
1040 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> | |
1041 <td id="LC78" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools index <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span></td> | |
1042 </tr> | |
1043 <tr> | |
1044 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> | |
1045 <td id="LC79" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>argstring = <span class="pl-pds">"</span></span> <span class="pl-k">+</span> argString)</td> | |
1046 </tr> | |
1047 <tr> | |
1048 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> | |
1049 <td id="LC80" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1050 </tr> | |
1051 <tr> | |
1052 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> | |
1053 <td id="LC81" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c"><span class="pl-c">#</span>we have saved out the relevent name.bam, name.sorted and name.sorted.bai files</span></td> | |
1054 </tr> | |
1055 <tr> | |
1056 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> | |
1057 <td id="LC82" class="blob-code blob-code-inner js-file-line"> | |
1058 </td> | |
1059 </tr> | |
1060 <tr> | |
1061 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> | |
1062 <td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> we will not have the .gtf file so call cufflinks without -G option</span></td> | |
1063 </tr> | |
1064 <tr> | |
1065 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> | |
1066 <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptAbundance</span>(<span class="pl-smi">inputname</span>):</td> | |
1067 </tr> | |
1068 <tr> | |
1069 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> | |
1070 <td id="LC85" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>cufflinks -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.cuff -u -p 8 <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span></td> | |
1071 </tr> | |
1072 <tr> | |
1073 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> | |
1074 <td id="LC86" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td> | |
1075 </tr> | |
1076 <tr> | |
1077 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> | |
1078 <td id="LC87" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span>remove name.sorted</span></td> | |
1079 </tr> | |
1080 <tr> | |
1081 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> | |
1082 <td id="LC88" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span>)</td> | |
1083 </tr> | |
1084 <tr> | |
1085 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> | |
1086 <td id="LC89" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span>)</td> | |
1087 </tr> | |
1088 <tr> | |
1089 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> | |
1090 <td id="LC90" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> | |
1091 </tr> | |
1092 <tr> | |
1093 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> | |
1094 <td id="LC91" class="blob-code blob-code-inner js-file-line"> | |
1095 </td> | |
1096 </tr> | |
1097 <tr> | |
1098 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> | |
1099 <td id="LC92" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptsForBlast</span>(<span class="pl-smi">name</span>, <span class="pl-smi">refFastq</span>):</td> | |
1100 </tr> | |
1101 <tr> | |
1102 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td> | |
1103 <td id="LC93" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> quick and dirty just to see.</span></td> | |
1104 </tr> | |
1105 <tr> | |
1106 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> | |
1107 <td id="LC94" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> | |
1108 </tr> | |
1109 <tr> | |
1110 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td> | |
1111 <td id="LC95" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> 'mydata/test.fasta' -> 'test'</span></td> | |
1112 </tr> | |
1113 <tr> | |
1114 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> | |
1115 <td id="LC96" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td> | |
1116 </tr> | |
1117 <tr> | |
1118 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> | |
1119 <td id="LC97" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> refBase <span class="pl-c"><span class="pl-c">#</span> eg refPath = data/Reference/Trinity/Trinity.fasta</span></td> | |
1120 </tr> | |
1121 <tr> | |
1122 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> | |
1123 <td id="LC98" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> used for dirty # refPath = 'Trinity.fasta' # dirty one</span></td> | |
1124 </tr> | |
1125 <tr> | |
1126 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> | |
1127 <td id="LC99" class="blob-code blob-code-inner js-file-line"> track_df <span class="pl-k">=</span> pd.read_csv(name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>.cuff/genes.fpkm_tracking<span class="pl-pds">'</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>)</td> | |
1128 </tr> | |
1129 <tr> | |
1130 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> | |
1131 <td id="LC100" class="blob-code blob-code-inner js-file-line"> names <span class="pl-k">=</span> track_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>]</td> | |
1132 </tr> | |
1133 <tr> | |
1134 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> | |
1135 <td id="LC101" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(len(names))</span></td> | |
1136 </tr> | |
1137 <tr> | |
1138 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> | |
1139 <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(names[:5])</span></td> | |
1140 </tr> | |
1141 <tr> | |
1142 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> | |
1143 <td id="LC103" class="blob-code blob-code-inner js-file-line"> | |
1144 </td> | |
1145 </tr> | |
1146 <tr> | |
1147 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> | |
1148 <td id="LC104" class="blob-code blob-code-inner js-file-line"> nlist <span class="pl-k">=</span> []</td> | |
1149 </tr> | |
1150 <tr> | |
1151 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> | |
1152 <td id="LC105" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(names)):</td> | |
1153 </tr> | |
1154 <tr> | |
1155 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> | |
1156 <td id="LC106" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> names[n].find(<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>)</td> | |
1157 </tr> | |
1158 <tr> | |
1159 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> | |
1160 <td id="LC107" class="blob-code blob-code-inner js-file-line"> nlist.append(names[n][:i])</td> | |
1161 </tr> | |
1162 <tr> | |
1163 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> | |
1164 <td id="LC108" class="blob-code blob-code-inner js-file-line"> nameset <span class="pl-k">=</span> <span class="pl-c1">set</span>(nlist) <span class="pl-c"><span class="pl-c">#</span>get unique.</span></td> | |
1165 </tr> | |
1166 <tr> | |
1167 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> | |
1168 <td id="LC109" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(refPath, <span class="pl-s"><span class="pl-pds">'</span>r<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> myRef:</td> | |
1169 </tr> | |
1170 <tr> | |
1171 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> | |
1172 <td id="LC110" class="blob-code blob-code-inner js-file-line"> refData <span class="pl-k">=</span> myRef.read()</td> | |
1173 </tr> | |
1174 <tr> | |
1175 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> | |
1176 <td id="LC111" class="blob-code blob-code-inner js-file-line"> refData<span class="pl-k">=</span> refData<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n</span>><span class="pl-pds">'</span></span></td> | |
1177 </tr> | |
1178 <tr> | |
1179 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> | |
1180 <td id="LC112" class="blob-code blob-code-inner js-file-line"> | |
1181 </td> | |
1182 </tr> | |
1183 <tr> | |
1184 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> | |
1185 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">'</span>_for_blast.fa<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> outfile:</td> | |
1186 </tr> | |
1187 <tr> | |
1188 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> | |
1189 <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> trans_id <span class="pl-k">in</span> nameset:</td> | |
1190 </tr> | |
1191 <tr> | |
1192 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> | |
1193 <td id="LC115" class="blob-code blob-code-inner js-file-line"> namepos <span class="pl-k">=</span> refData.find(trans_id)</td> | |
1194 </tr> | |
1195 <tr> | |
1196 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> | |
1197 <td id="LC116" class="blob-code blob-code-inner js-file-line"> endpos <span class="pl-k">=</span> refData.find(<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>, namepos)</td> | |
1198 </tr> | |
1199 <tr> | |
1200 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> | |
1201 <td id="LC117" class="blob-code blob-code-inner js-file-line"> outfile.write(<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span><span class="pl-k">+</span>refData[namepos:endpos])</td> | |
1202 </tr> | |
1203 <tr> | |
1204 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> | |
1205 <td id="LC118" class="blob-code blob-code-inner js-file-line"> | |
1206 </td> | |
1207 </tr> | |
1208 <tr> | |
1209 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> | |
1210 <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> | |
1211 </tr> | |
1212 <tr> | |
1213 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td> | |
1214 <td id="LC120" class="blob-code blob-code-inner js-file-line"> | |
1215 </td> | |
1216 </tr> | |
1217 <tr> | |
1218 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> | |
1219 <td id="LC121" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">html_resource</span>, <span class="pl-smi">database</span>):</td> | |
1220 </tr> | |
1221 <tr> | |
1222 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> | |
1223 <td id="LC122" class="blob-code blob-code-inner js-file-line"> db_path <span class="pl-k">=</span> database</td> | |
1224 </tr> | |
1225 <tr> | |
1226 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> | |
1227 <td id="LC123" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>blastx -db <span class="pl-pds">"</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -query <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_for_blast.fa -outfmt 10 -out <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span></td> | |
1228 </tr> | |
1229 <tr> | |
1230 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> | |
1231 <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> | |
1232 </tr> | |
1233 <tr> | |
1234 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> | |
1235 <td id="LC125" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1236 </tr> | |
1237 <tr> | |
1238 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> | |
1239 <td id="LC126" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> | |
1240 </tr> | |
1241 <tr> | |
1242 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> | |
1243 <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in blastall<span class="pl-pds">"</span></span></td> | |
1244 </tr> | |
1245 <tr> | |
1246 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> | |
1247 <td id="LC128" class="blob-code blob-code-inner js-file-line"> blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span>)</td> | |
1248 </tr> | |
1249 <tr> | |
1250 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> | |
1251 <td id="LC129" class="blob-code blob-code-inner js-file-line"> blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>mismatch<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>gapopen<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qend<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>sstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>send<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]</td> | |
1252 </tr> | |
1253 <tr> | |
1254 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> | |
1255 <td id="LC130" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]<span class="pl-k">>=</span><span class="pl-c1">70</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">100</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>] <span class="pl-k"><=</span><span class="pl-c1">0.001</span>) ]</td> | |
1256 </tr> | |
1257 <tr> | |
1258 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> | |
1259 <td id="LC131" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]] <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td> | |
1260 </tr> | |
1261 <tr> | |
1262 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> | |
1263 <td id="LC132" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> need to allocate the transcripts (if allocated more than once to the phylotype with least error.</span></td> | |
1264 </tr> | |
1265 <tr> | |
1266 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> | |
1267 <td id="LC133" class="blob-code blob-code-inner js-file-line"> transcripts <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>]</td> | |
1268 </tr> | |
1269 <tr> | |
1270 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> | |
1271 <td id="LC134" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>])</td> | |
1272 </tr> | |
1273 <tr> | |
1274 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> | |
1275 <td id="LC135" class="blob-code blob-code-inner js-file-line"> transSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(transcripts)</td> | |
1276 </tr> | |
1277 <tr> | |
1278 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> | |
1279 <td id="LC136" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> t <span class="pl-k">in</span> transSet:</td> | |
1280 </tr> | |
1281 <tr> | |
1282 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> | |
1283 <td id="LC137" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> blastResult_df[(blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> t)]</td> | |
1284 </tr> | |
1285 <tr> | |
1286 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> | |
1287 <td id="LC138" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get one with smallest error value</span></td> | |
1288 </tr> | |
1289 <tr> | |
1290 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> | |
1291 <td id="LC139" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(t + ":")</span></td> | |
1292 </tr> | |
1293 <tr> | |
1294 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> | |
1295 <td id="LC140" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(temp_df)</span></td> | |
1296 </tr> | |
1297 <tr> | |
1298 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> | |
1299 <td id="LC141" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> temp_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>])</td> | |
1300 </tr> | |
1301 <tr> | |
1302 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> | |
1303 <td id="LC142" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> b_df.append(temp_df.iloc[[<span class="pl-c1">0</span>]])</td> | |
1304 </tr> | |
1305 <tr> | |
1306 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td> | |
1307 <td id="LC143" class="blob-code blob-code-inner js-file-line"> | |
1308 </td> | |
1309 </tr> | |
1310 <tr> | |
1311 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td> | |
1312 <td id="LC144" class="blob-code blob-code-inner js-file-line"> b_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>])</td> | |
1313 </tr> | |
1314 <tr> | |
1315 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td> | |
1316 <td id="LC145" class="blob-code blob-code-inner js-file-line"> b_df.to_csv(test_name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">'</span>_transcript.csv<span class="pl-pds">'</span></span>)</td> | |
1317 </tr> | |
1318 <tr> | |
1319 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td> | |
1320 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> b_df</td> | |
1321 </tr> | |
1322 <tr> | |
1323 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td> | |
1324 <td id="LC147" class="blob-code blob-code-inner js-file-line"> | |
1325 </td> | |
1326 </tr> | |
1327 <tr> | |
1328 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td> | |
1329 <td id="LC148" class="blob-code blob-code-inner js-file-line"> | |
1330 </td> | |
1331 </tr> | |
1332 <tr> | |
1333 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td> | |
1334 <td id="LC149" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createMultiHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">composite_df</span>):</td> | |
1335 </tr> | |
1336 <tr> | |
1337 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td> | |
1338 <td id="LC150" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td> | |
1339 </tr> | |
1340 <tr> | |
1341 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td> | |
1342 <td id="LC151" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span></title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td> | |
1343 </tr> | |
1344 <tr> | |
1345 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td> | |
1346 <td id="LC152" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Sample name: <span class="pl-pds">"</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]</td> | |
1347 </tr> | |
1348 <tr> | |
1349 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td> | |
1350 <td id="LC153" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td> | |
1351 </tr> | |
1352 <tr> | |
1353 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td> | |
1354 <td id="LC154" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Legend: <span class="pl-pds">"</span></span> \</td> | |
1355 </tr> | |
1356 <tr> | |
1357 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td> | |
1358 <td id="LC155" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptomes. <span class="pl-pds">"</span></span> \</td> | |
1359 </tr> | |
1360 <tr> | |
1361 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td> | |
1362 <td id="LC156" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">"</span></span> \</td> | |
1363 </tr> | |
1364 <tr> | |
1365 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td> | |
1366 <td id="LC157" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">"</span></span> \</td> | |
1367 </tr> | |
1368 <tr> | |
1369 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td> | |
1370 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">"</span></span> \</td> | |
1371 </tr> | |
1372 <tr> | |
1373 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td> | |
1374 <td id="LC159" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>(Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td> | |
1375 </tr> | |
1376 <tr> | |
1377 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td> | |
1378 <td id="LC160" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td> | |
1379 </tr> | |
1380 <tr> | |
1381 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td> | |
1382 <td id="LC161" class="blob-code blob-code-inner js-file-line"> | |
1383 </td> | |
1384 </tr> | |
1385 <tr> | |
1386 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td> | |
1387 <td id="LC162" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><span class="pl-pds">"</span></span></td> | |
1388 </tr> | |
1389 <tr> | |
1390 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td> | |
1391 <td id="LC163" class="blob-code blob-code-inner js-file-line"> wLists <span class="pl-k">=</span> []</td> | |
1392 </tr> | |
1393 <tr> | |
1394 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td> | |
1395 <td id="LC164" class="blob-code blob-code-inner js-file-line"> | |
1396 </td> | |
1397 </tr> | |
1398 <tr> | |
1399 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td> | |
1400 <td id="LC165" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>,<span class="pl-c1">len</span>(labelList)):</td> | |
1401 </tr> | |
1402 <tr> | |
1403 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td> | |
1404 <td id="LC166" class="blob-code blob-code-inner js-file-line"> wLists.append(composite_df[labelList[j]])</td> | |
1405 </tr> | |
1406 <tr> | |
1407 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td> | |
1408 <td id="LC167" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><th><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(labelList[j]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></th><span class="pl-pds">"</span></span></td> | |
1409 </tr> | |
1410 <tr> | |
1411 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td> | |
1412 <td id="LC168" class="blob-code blob-code-inner js-file-line"> | |
1413 </td> | |
1414 </tr> | |
1415 <tr> | |
1416 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td> | |
1417 <td id="LC169" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">+</span> header</td> | |
1418 </tr> | |
1419 <tr> | |
1420 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td> | |
1421 <td id="LC170" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> | |
1422 </tr> | |
1423 <tr> | |
1424 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td> | |
1425 <td id="LC171" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> composite_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> | |
1426 </tr> | |
1427 <tr> | |
1428 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td> | |
1429 <td id="LC172" class="blob-code blob-code-inner js-file-line"> | |
1430 </td> | |
1431 </tr> | |
1432 <tr> | |
1433 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td> | |
1434 <td id="LC173" class="blob-code blob-code-inner js-file-line"> | |
1435 </td> | |
1436 </tr> | |
1437 <tr> | |
1438 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td> | |
1439 <td id="LC174" class="blob-code blob-code-inner js-file-line"> | |
1440 </td> | |
1441 </tr> | |
1442 <tr> | |
1443 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td> | |
1444 <td id="LC175" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(composite_df)):</td> | |
1445 </tr> | |
1446 <tr> | |
1447 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td> | |
1448 <td id="LC176" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phyList[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><span class="pl-pds">"</span></span></td> | |
1449 </tr> | |
1450 <tr> | |
1451 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td> | |
1452 <td id="LC177" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span>):</td> | |
1453 </tr> | |
1454 <tr> | |
1455 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td> | |
1456 <td id="LC178" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(j)</span></td> | |
1457 </tr> | |
1458 <tr> | |
1459 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td> | |
1460 <td id="LC179" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(wLists[j][i], <span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td> | |
1461 </tr> | |
1462 <tr> | |
1463 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td> | |
1464 <td id="LC180" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><span class="pl-pds">"</span></span></td> | |
1465 </tr> | |
1466 <tr> | |
1467 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td> | |
1468 <td id="LC181" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-cce">\n</span><span class="pl-pds">"</span></span></td> | |
1469 </tr> | |
1470 <tr> | |
1471 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td> | |
1472 <td id="LC182" class="blob-code blob-code-inner js-file-line"> | |
1473 </td> | |
1474 </tr> | |
1475 <tr> | |
1476 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td> | |
1477 <td id="LC183" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td> | |
1478 </tr> | |
1479 <tr> | |
1480 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td> | |
1481 <td id="LC184" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span></h3><span class="pl-pds">"</span></span></td> | |
1482 </tr> | |
1483 <tr> | |
1484 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td> | |
1485 <td id="LC185" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> | |
1486 </tr> | |
1487 <tr> | |
1488 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td> | |
1489 <td id="LC186" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> | |
1490 </tr> | |
1491 <tr> | |
1492 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td> | |
1493 <td id="LC187" class="blob-code blob-code-inner js-file-line"> | |
1494 </td> | |
1495 </tr> | |
1496 <tr> | |
1497 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td> | |
1498 <td id="LC188" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td> | |
1499 </tr> | |
1500 <tr> | |
1501 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td> | |
1502 <td id="LC189" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> | |
1503 </tr> | |
1504 <tr> | |
1505 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td> | |
1506 <td id="LC190" class="blob-code blob-code-inner js-file-line"> | |
1507 </td> | |
1508 </tr> | |
1509 <tr> | |
1510 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td> | |
1511 <td id="LC191" class="blob-code blob-code-inner js-file-line"> | |
1512 </td> | |
1513 </tr> | |
1514 <tr> | |
1515 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td> | |
1516 <td id="LC192" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">sum_df</span>):</td> | |
1517 </tr> | |
1518 <tr> | |
1519 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td> | |
1520 <td id="LC193" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td> | |
1521 </tr> | |
1522 <tr> | |
1523 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td> | |
1524 <td id="LC194" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span></title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td> | |
1525 </tr> | |
1526 <tr> | |
1527 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td> | |
1528 <td id="LC195" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Sample name: <span class="pl-pds">"</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]</td> | |
1529 </tr> | |
1530 <tr> | |
1531 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td> | |
1532 <td id="LC196" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td> | |
1533 </tr> | |
1534 <tr> | |
1535 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td> | |
1536 <td id="LC197" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Legend: <span class="pl-pds">"</span></span> \</td> | |
1537 </tr> | |
1538 <tr> | |
1539 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td> | |
1540 <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptome. <span class="pl-pds">"</span></span> \</td> | |
1541 </tr> | |
1542 <tr> | |
1543 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td> | |
1544 <td id="LC199" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">"</span></span> \</td> | |
1545 </tr> | |
1546 <tr> | |
1547 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td> | |
1548 <td id="LC200" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">"</span></span> \</td> | |
1549 </tr> | |
1550 <tr> | |
1551 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td> | |
1552 <td id="LC201" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">"</span></span> \</td> | |
1553 </tr> | |
1554 <tr> | |
1555 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td> | |
1556 <td id="LC202" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>(Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td> | |
1557 </tr> | |
1558 <tr> | |
1559 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td> | |
1560 <td id="LC203" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td> | |
1561 </tr> | |
1562 <tr> | |
1563 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td> | |
1564 <td id="LC204" class="blob-code blob-code-inner js-file-line"> | |
1565 </td> | |
1566 </tr> | |
1567 <tr> | |
1568 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td> | |
1569 <td id="LC205" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;table-layout: auto; margin-left:25%;text-align:center'><tr><th>Phylotype</th><span class="pl-pds">"</span></span> \</td> | |
1570 </tr> | |
1571 <tr> | |
1572 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td> | |
1573 <td id="LC206" class="blob-code blob-code-inner js-file-line"> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><th>Combined FPKM</th><th>Weighted Frequency</th></tr><span class="pl-pds">"</span></span></td> | |
1574 </tr> | |
1575 <tr> | |
1576 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td> | |
1577 <td id="LC207" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> | |
1578 </tr> | |
1579 <tr> | |
1580 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td> | |
1581 <td id="LC208" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></td> | |
1582 </tr> | |
1583 <tr> | |
1584 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td> | |
1585 <td id="LC209" class="blob-code blob-code-inner js-file-line"> phySeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> | |
1586 </tr> | |
1587 <tr> | |
1588 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td> | |
1589 <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> sacSeries = sum_df['saccver']</span></td> | |
1590 </tr> | |
1591 <tr> | |
1592 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td> | |
1593 <td id="LC211" class="blob-code blob-code-inner js-file-line"> fSeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>]</td> | |
1594 </tr> | |
1595 <tr> | |
1596 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td> | |
1597 <td id="LC212" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> fSeries.sum()</td> | |
1598 </tr> | |
1599 <tr> | |
1600 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td> | |
1601 <td id="LC213" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print("Total="+str(total))</span></td> | |
1602 </tr> | |
1603 <tr> | |
1604 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td> | |
1605 <td id="LC214" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum_df)):</td> | |
1606 </tr> | |
1607 <tr> | |
1608 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td> | |
1609 <td id="LC215" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(phySeries[i])</span></td> | |
1610 </tr> | |
1611 <tr> | |
1612 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td> | |
1613 <td id="LC216" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i], <span class="pl-s"><span class="pl-pds">'</span>.2f<span class="pl-pds">'</span></span>)</td> | |
1614 </tr> | |
1615 <tr> | |
1616 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td> | |
1617 <td id="LC217" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i]<span class="pl-k">/</span>total, <span class="pl-s"><span class="pl-pds">'</span>.2f<span class="pl-pds">'</span></span>)</td> | |
1618 </tr> | |
1619 <tr> | |
1620 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td> | |
1621 <td id="LC218" class="blob-code blob-code-inner js-file-line"> | |
1622 </td> | |
1623 </tr> | |
1624 <tr> | |
1625 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td> | |
1626 <td id="LC219" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>w = format(weightList[i], '.4f')</span></td> | |
1627 </tr> | |
1628 <tr> | |
1629 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td> | |
1630 <td id="LC220" class="blob-code blob-code-inner js-file-line"> | |
1631 </td> | |
1632 </tr> | |
1633 <tr> | |
1634 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td> | |
1635 <td id="LC221" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phySeries[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(w)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-pds">"</span></span></td> | |
1636 </tr> | |
1637 <tr> | |
1638 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td> | |
1639 <td id="LC222" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td> | |
1640 </tr> | |
1641 <tr> | |
1642 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td> | |
1643 <td id="LC223" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span></h3><span class="pl-pds">"</span></span></td> | |
1644 </tr> | |
1645 <tr> | |
1646 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td> | |
1647 <td id="LC224" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> | |
1648 </tr> | |
1649 <tr> | |
1650 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td> | |
1651 <td id="LC225" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> | |
1652 </tr> | |
1653 <tr> | |
1654 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td> | |
1655 <td id="LC226" class="blob-code blob-code-inner js-file-line"> | |
1656 </td> | |
1657 </tr> | |
1658 <tr> | |
1659 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td> | |
1660 <td id="LC227" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td> | |
1661 </tr> | |
1662 <tr> | |
1663 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td> | |
1664 <td id="LC228" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> | |
1665 </tr> | |
1666 <tr> | |
1667 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td> | |
1668 <td id="LC229" class="blob-code blob-code-inner js-file-line"> | |
1669 </td> | |
1670 </tr> | |
1671 <tr> | |
1672 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td> | |
1673 <td id="LC230" class="blob-code blob-code-inner js-file-line"> | |
1674 </td> | |
1675 </tr> | |
1676 <tr> | |
1677 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td> | |
1678 <td id="LC231" class="blob-code blob-code-inner js-file-line"> | |
1679 </td> | |
1680 </tr> | |
1681 <tr> | |
1682 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td> | |
1683 <td id="LC232" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getPhyloNumber</span>(<span class="pl-smi">sac</span>):</td> | |
1684 </tr> | |
1685 <tr> | |
1686 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td> | |
1687 <td id="LC233" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> sac.find(<span class="pl-s"><span class="pl-pds">'</span>_<span class="pl-pds">'</span></span>)</td> | |
1688 </tr> | |
1689 <tr> | |
1690 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td> | |
1691 <td id="LC234" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c1">int</span>(sac[<span class="pl-c1">1</span>:i])</td> | |
1692 </tr> | |
1693 <tr> | |
1694 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td> | |
1695 <td id="LC235" class="blob-code blob-code-inner js-file-line"> | |
1696 </td> | |
1697 </tr> | |
1698 <tr> | |
1699 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td> | |
1700 <td id="LC236" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">combineFPMK</span>(<span class="pl-smi">tdict</span>):</td> | |
1701 </tr> | |
1702 <tr> | |
1703 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td> | |
1704 <td id="LC237" class="blob-code blob-code-inner js-file-line"> fpkm_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>.cuff/genes.fpkm_tracking<span class="pl-pds">'</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>)</td> | |
1705 </tr> | |
1706 <tr> | |
1707 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td> | |
1708 <td id="LC238" class="blob-code blob-code-inner js-file-line"> | |
1709 </td> | |
1710 </tr> | |
1711 <tr> | |
1712 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td> | |
1713 <td id="LC239" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t')</span></td> | |
1714 </tr> | |
1715 <tr> | |
1716 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td> | |
1717 <td id="LC240" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td> | |
1718 </tr> | |
1719 <tr> | |
1720 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td> | |
1721 <td id="LC241" class="blob-code blob-code-inner js-file-line"> fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>].apply(<span class="pl-k">lambda</span> <span class="pl-smi">names</span>: names[:names.find(<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>)])</td> | |
1722 </tr> | |
1723 <tr> | |
1724 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td> | |
1725 <td id="LC242" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td> | |
1726 </tr> | |
1727 <tr> | |
1728 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td> | |
1729 <td id="LC243" class="blob-code blob-code-inner js-file-line"> reducedBlast_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>_transcript.csv<span class="pl-pds">'</span></span>)</td> | |
1730 </tr> | |
1731 <tr> | |
1732 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td> | |
1733 <td id="LC244" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> reducedBlast_df = pd.read_csv('TrinityVT_transcript.csv')</span></td> | |
1734 </tr> | |
1735 <tr> | |
1736 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td> | |
1737 <td id="LC245" class="blob-code blob-code-inner js-file-line"> saccverSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(reducedBlast_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>])</td> | |
1738 </tr> | |
1739 <tr> | |
1740 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td> | |
1741 <td id="LC246" class="blob-code blob-code-inner js-file-line"> saccverList <span class="pl-k">=</span> <span class="pl-c1">list</span>(saccverSet)</td> | |
1742 </tr> | |
1743 <tr> | |
1744 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td> | |
1745 <td id="LC247" class="blob-code blob-code-inner js-file-line"> saccverList.sort()</td> | |
1746 </tr> | |
1747 <tr> | |
1748 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td> | |
1749 <td id="LC248" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(saccverList[:5])</span></td> | |
1750 </tr> | |
1751 <tr> | |
1752 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td> | |
1753 <td id="LC249" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>])</td> | |
1754 </tr> | |
1755 <tr> | |
1756 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td> | |
1757 <td id="LC250" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> sv <span class="pl-k">in</span> saccverList:</td> | |
1758 </tr> | |
1759 <tr> | |
1760 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td> | |
1761 <td id="LC251" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(sv)</span></td> | |
1762 </tr> | |
1763 <tr> | |
1764 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td> | |
1765 <td id="LC252" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> reducedBlast_df[reducedBlast_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> sv]</td> | |
1766 </tr> | |
1767 <tr> | |
1768 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td> | |
1769 <td id="LC253" class="blob-code blob-code-inner js-file-line"> qList <span class="pl-k">=</span> <span class="pl-c1">list</span>(temp_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>])</td> | |
1770 </tr> | |
1771 <tr> | |
1772 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td> | |
1773 <td id="LC254" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> q <span class="pl-k">in</span> qList:</td> | |
1774 </tr> | |
1775 <tr> | |
1776 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td> | |
1777 <td id="LC255" class="blob-code blob-code-inner js-file-line"> f_df <span class="pl-k">=</span> fpkm_df[(fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> q)]</td> | |
1778 </tr> | |
1779 <tr> | |
1780 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td> | |
1781 <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-c1">len</span>(f_df) <span class="pl-k">></span> <span class="pl-c1">1</span>:</td> | |
1782 </tr> | |
1783 <tr> | |
1784 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td> | |
1785 <td id="LC257" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">'</span>WARNING MULTIPLE FPKM<span class="pl-pds">'</span></span>)</td> | |
1786 </tr> | |
1787 <tr> | |
1788 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td> | |
1789 <td id="LC258" class="blob-code blob-code-inner js-file-line"> new_fpkm<span class="pl-k">=</span><span class="pl-c1">list</span>(f_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>])</td> | |
1790 </tr> | |
1791 <tr> | |
1792 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td> | |
1793 <td id="LC259" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> (new_fpkm[<span class="pl-c1">0</span>])</td> | |
1794 </tr> | |
1795 <tr> | |
1796 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td> | |
1797 <td id="LC260" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(f)</span></td> | |
1798 </tr> | |
1799 <tr> | |
1800 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td> | |
1801 <td id="LC261" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> new_df.append({<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>: q, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>: sv, <span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>: f}, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1802 </tr> | |
1803 <tr> | |
1804 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td> | |
1805 <td id="LC262" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> new_df.groupby(<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum().reset_index()</td> | |
1806 </tr> | |
1807 <tr> | |
1808 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td> | |
1809 <td id="LC263" class="blob-code blob-code-inner js-file-line"> | |
1810 </td> | |
1811 </tr> | |
1812 <tr> | |
1813 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td> | |
1814 <td id="LC264" class="blob-code blob-code-inner js-file-line"> FPKMsum_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> FPKMsum_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: getPhyloNumber(row[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>]), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> | |
1815 </tr> | |
1816 <tr> | |
1817 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td> | |
1818 <td id="LC265" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> | |
1819 </tr> | |
1820 <tr> | |
1821 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td> | |
1822 <td id="LC266" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.reset_index(<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1823 </tr> | |
1824 <tr> | |
1825 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td> | |
1826 <td id="LC267" class="blob-code blob-code-inner js-file-line"> | |
1827 </td> | |
1828 </tr> | |
1829 <tr> | |
1830 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td> | |
1831 <td id="LC268" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum_df)</span></td> | |
1832 </tr> | |
1833 <tr> | |
1834 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td> | |
1835 <td id="LC269" class="blob-code blob-code-inner js-file-line"> FPKMsum_df.to_csv(<span class="pl-s"><span class="pl-pds">'</span>FPKM_sum.csv<span class="pl-pds">'</span></span>)</td> | |
1836 </tr> | |
1837 <tr> | |
1838 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td> | |
1839 <td id="LC270" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum_df.groupby(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum().reset_index()</td> | |
1840 </tr> | |
1841 <tr> | |
1842 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td> | |
1843 <td id="LC271" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum2_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> | |
1844 </tr> | |
1845 <tr> | |
1846 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td> | |
1847 <td id="LC272" class="blob-code blob-code-inner js-file-line"> | |
1848 </td> | |
1849 </tr> | |
1850 <tr> | |
1851 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td> | |
1852 <td id="LC273" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum2_df)</span></td> | |
1853 </tr> | |
1854 <tr> | |
1855 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td> | |
1856 <td id="LC274" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df.to_csv(<span class="pl-s"><span class="pl-pds">'</span>FPKM_sum2.csv<span class="pl-pds">'</span></span>) <span class="pl-c"><span class="pl-c">#</span> in case more than one entry for a particular phylotype</span></td> | |
1857 </tr> | |
1858 <tr> | |
1859 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td> | |
1860 <td id="LC275" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> FPKMsum_df, FPKMsum2_df</td> | |
1861 </tr> | |
1862 <tr> | |
1863 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td> | |
1864 <td id="LC276" class="blob-code blob-code-inner js-file-line"> | |
1865 </td> | |
1866 </tr> | |
1867 <tr> | |
1868 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td> | |
1869 <td id="LC277" class="blob-code blob-code-inner js-file-line"> | |
1870 </td> | |
1871 </tr> | |
1872 <tr> | |
1873 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td> | |
1874 <td id="LC278" class="blob-code blob-code-inner js-file-line"> | |
1875 </td> | |
1876 </tr> | |
1877 <tr> | |
1878 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td> | |
1879 <td id="LC279" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">normalisef</span>(<span class="pl-smi">f</span>,<span class="pl-smi">max</span>):</td> | |
1880 </tr> | |
1881 <tr> | |
1882 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td> | |
1883 <td id="LC280" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> f<span class="pl-k">/</span><span class="pl-c1">max</span></td> | |
1884 </tr> | |
1885 <tr> | |
1886 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td> | |
1887 <td id="LC281" class="blob-code blob-code-inner js-file-line"> | |
1888 </td> | |
1889 </tr> | |
1890 <tr> | |
1891 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td> | |
1892 <td id="LC282" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getComposite_sum2</span>(<span class="pl-smi">nameList</span>,<span class="pl-smi">sum2_dfs</span>):</td> | |
1893 </tr> | |
1894 <tr> | |
1895 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td> | |
1896 <td id="LC283" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> lets get a composite sum2_df from all of the sum2_dfs</span></td> | |
1897 </tr> | |
1898 <tr> | |
1899 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td> | |
1900 <td id="LC284" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> []</td> | |
1901 </tr> | |
1902 <tr> | |
1903 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td> | |
1904 <td id="LC285" class="blob-code blob-code-inner js-file-line"> | |
1905 </td> | |
1906 </tr> | |
1907 <tr> | |
1908 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td> | |
1909 <td id="LC286" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td> | |
1910 </tr> | |
1911 <tr> | |
1912 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td> | |
1913 <td id="LC287" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum()</td> | |
1914 </tr> | |
1915 <tr> | |
1916 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td> | |
1917 <td id="LC288" class="blob-code blob-code-inner js-file-line"> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_dfs[i].apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], total), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> | |
1918 </tr> | |
1919 <tr> | |
1920 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td> | |
1921 <td id="LC289" class="blob-code blob-code-inner js-file-line"> pSeries <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> | |
1922 </tr> | |
1923 <tr> | |
1924 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td> | |
1925 <td id="LC290" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pSeries:</td> | |
1926 </tr> | |
1927 <tr> | |
1928 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td> | |
1929 <td id="LC291" class="blob-code blob-code-inner js-file-line"> phyList.append(p) <span class="pl-c"><span class="pl-c">#</span> get all the phylotypes in this one</span></td> | |
1930 </tr> | |
1931 <tr> | |
1932 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td> | |
1933 <td id="LC292" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> <span class="pl-c1">list</span>(<span class="pl-c1">set</span>(phyList))</td> | |
1934 </tr> | |
1935 <tr> | |
1936 <td id="L293" class="blob-num js-line-number" data-line-number="293"></td> | |
1937 <td id="LC293" class="blob-code blob-code-inner js-file-line"> phyList.sort()</td> | |
1938 </tr> | |
1939 <tr> | |
1940 <td id="L294" class="blob-num js-line-number" data-line-number="294"></td> | |
1941 <td id="LC294" class="blob-code blob-code-inner js-file-line"> composite_sum2_df <span class="pl-k">=</span> pd.DataFrame(phyList, <span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> | |
1942 </tr> | |
1943 <tr> | |
1944 <td id="L295" class="blob-num js-line-number" data-line-number="295"></td> | |
1945 <td id="LC295" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td> | |
1946 </tr> | |
1947 <tr> | |
1948 <td id="L296" class="blob-num js-line-number" data-line-number="296"></td> | |
1949 <td id="LC296" class="blob-code blob-code-inner js-file-line"> wList <span class="pl-k">=</span> []</td> | |
1950 </tr> | |
1951 <tr> | |
1952 <td id="L297" class="blob-num js-line-number" data-line-number="297"></td> | |
1953 <td id="LC297" class="blob-code blob-code-inner js-file-line"> pindf <span class="pl-k">=</span> <span class="pl-c1">list</span>(sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> | |
1954 </tr> | |
1955 <tr> | |
1956 <td id="L298" class="blob-num js-line-number" data-line-number="298"></td> | |
1957 <td id="LC298" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(pindf)</span></td> | |
1958 </tr> | |
1959 <tr> | |
1960 <td id="L299" class="blob-num js-line-number" data-line-number="299"></td> | |
1961 <td id="LC299" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> phyList:</td> | |
1962 </tr> | |
1963 <tr> | |
1964 <td id="L300" class="blob-num js-line-number" data-line-number="300"></td> | |
1965 <td id="LC300" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> p <span class="pl-k">in</span> pindf:</td> | |
1966 </tr> | |
1967 <tr> | |
1968 <td id="L301" class="blob-num js-line-number" data-line-number="301"></td> | |
1969 <td id="LC301" class="blob-code blob-code-inner js-file-line"> df <span class="pl-k">=</span> sum2_dfs[i]</td> | |
1970 </tr> | |
1971 <tr> | |
1972 <td id="L302" class="blob-num js-line-number" data-line-number="302"></td> | |
1973 <td id="LC302" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> df.loc[df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> p, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>].iloc[<span class="pl-c1">0</span>]</td> | |
1974 </tr> | |
1975 <tr> | |
1976 <td id="L303" class="blob-num js-line-number" data-line-number="303"></td> | |
1977 <td id="LC303" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> | |
1978 </tr> | |
1979 <tr> | |
1980 <td id="L304" class="blob-num js-line-number" data-line-number="304"></td> | |
1981 <td id="LC304" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">0</span></td> | |
1982 </tr> | |
1983 <tr> | |
1984 <td id="L305" class="blob-num js-line-number" data-line-number="305"></td> | |
1985 <td id="LC305" class="blob-code blob-code-inner js-file-line"> wList.append(w)</td> | |
1986 </tr> | |
1987 <tr> | |
1988 <td id="L306" class="blob-num js-line-number" data-line-number="306"></td> | |
1989 <td id="LC306" class="blob-code blob-code-inner js-file-line"> composite_sum2_df[nameList[i]] <span class="pl-k">=</span> wList</td> | |
1990 </tr> | |
1991 <tr> | |
1992 <td id="L307" class="blob-num js-line-number" data-line-number="307"></td> | |
1993 <td id="LC307" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(composite_sum2_df)</span></td> | |
1994 </tr> | |
1995 <tr> | |
1996 <td id="L308" class="blob-num js-line-number" data-line-number="308"></td> | |
1997 <td id="LC308" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>composite_sum2_df.to_csv('composite.csv')</span></td> | |
1998 </tr> | |
1999 <tr> | |
2000 <td id="L309" class="blob-num js-line-number" data-line-number="309"></td> | |
2001 <td id="LC309" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> composite_sum2_df</td> | |
2002 </tr> | |
2003 <tr> | |
2004 <td id="L310" class="blob-num js-line-number" data-line-number="310"></td> | |
2005 <td id="LC310" class="blob-code blob-code-inner js-file-line"> | |
2006 </td> | |
2007 </tr> | |
2008 <tr> | |
2009 <td id="L311" class="blob-num js-line-number" data-line-number="311"></td> | |
2010 <td id="LC311" class="blob-code blob-code-inner js-file-line"> | |
2011 </td> | |
2012 </tr> | |
2013 <tr> | |
2014 <td id="L312" class="blob-num js-line-number" data-line-number="312"></td> | |
2015 <td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doMultiBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">composite_df</span>): <span class="pl-c"><span class="pl-c">#</span>array of multiple sum2_dfs</span></td> | |
2016 </tr> | |
2017 <tr> | |
2018 <td id="L313" class="blob-num js-line-number" data-line-number="313"></td> | |
2019 <td id="LC313" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td> | |
2020 </tr> | |
2021 <tr> | |
2022 <td id="L314" class="blob-num js-line-number" data-line-number="314"></td> | |
2023 <td id="LC314" class="blob-code blob-code-inner js-file-line"> sampnum <span class="pl-k">=</span> <span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span></td> | |
2024 </tr> | |
2025 <tr> | |
2026 <td id="L315" class="blob-num js-line-number" data-line-number="315"></td> | |
2027 <td id="LC315" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> need to arrange bars</span></td> | |
2028 </tr> | |
2029 <tr> | |
2030 <td id="L316" class="blob-num js-line-number" data-line-number="316"></td> | |
2031 <td id="LC316" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> number of phylotype = len(composite_df)</span></td> | |
2032 </tr> | |
2033 <tr> | |
2034 <td id="L317" class="blob-num js-line-number" data-line-number="317"></td> | |
2035 <td id="LC317" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>number of bars = (len(labelist)-1) +1 for space</span></td> | |
2036 </tr> | |
2037 <tr> | |
2038 <td id="L318" class="blob-num js-line-number" data-line-number="318"></td> | |
2039 <td id="LC318" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> ytick needs to ne</span></td> | |
2040 </tr> | |
2041 <tr> | |
2042 <td id="L319" class="blob-num js-line-number" data-line-number="319"></td> | |
2043 <td id="LC319" class="blob-code blob-code-inner js-file-line"> | |
2044 </td> | |
2045 </tr> | |
2046 <tr> | |
2047 <td id="L320" class="blob-num js-line-number" data-line-number="320"></td> | |
2048 <td id="LC320" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab10<span class="pl-pds">'</span></span>)</td> | |
2049 </tr> | |
2050 <tr> | |
2051 <td id="L321" class="blob-num js-line-number" data-line-number="321"></td> | |
2052 <td id="LC321" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td> | |
2053 </tr> | |
2054 <tr> | |
2055 <td id="L322" class="blob-num js-line-number" data-line-number="322"></td> | |
2056 <td id="LC322" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptomes. <span class="pl-pds">"</span></span> \</td> | |
2057 </tr> | |
2058 <tr> | |
2059 <td id="L323" class="blob-num js-line-number" data-line-number="323"></td> | |
2060 <td id="LC323" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">"</span></span> \</td> | |
2061 </tr> | |
2062 <tr> | |
2063 <td id="L324" class="blob-num js-line-number" data-line-number="324"></td> | |
2064 <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>for combined transcript abundance. <span class="pl-pds">"</span></span> \</td> | |
2065 </tr> | |
2066 <tr> | |
2067 <td id="L325" class="blob-num js-line-number" data-line-number="325"></td> | |
2068 <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> | |
2069 </tr> | |
2070 <tr> | |
2071 <td id="L326" class="blob-num js-line-number" data-line-number="326"></td> | |
2072 <td id="LC326" class="blob-code blob-code-inner js-file-line"> width <span class="pl-k">=</span> <span class="pl-c1">0.6</span></td> | |
2073 </tr> | |
2074 <tr> | |
2075 <td id="L327" class="blob-num js-line-number" data-line-number="327"></td> | |
2076 <td id="LC327" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> np.arange(width<span class="pl-k">*</span>sampnum<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>))</td> | |
2077 </tr> | |
2078 <tr> | |
2079 <td id="L328" class="blob-num js-line-number" data-line-number="328"></td> | |
2080 <td id="LC328" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(ind)</span></td> | |
2081 </tr> | |
2082 <tr> | |
2083 <td id="L329" class="blob-num js-line-number" data-line-number="329"></td> | |
2084 <td id="LC329" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span><span class="pl-c1">0.4</span></td> | |
2085 </tr> | |
2086 <tr> | |
2087 <td id="L330" class="blob-num js-line-number" data-line-number="330"></td> | |
2088 <td id="LC330" class="blob-code blob-code-inner js-file-line"> | |
2089 </td> | |
2090 </tr> | |
2091 <tr> | |
2092 <td id="L331" class="blob-num js-line-number" data-line-number="331"></td> | |
2093 <td id="LC331" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td> | |
2094 </tr> | |
2095 <tr> | |
2096 <td id="L332" class="blob-num js-line-number" data-line-number="332"></td> | |
2097 <td id="LC332" class="blob-code blob-code-inner js-file-line"> | |
2098 </td> | |
2099 </tr> | |
2100 <tr> | |
2101 <td id="L333" class="blob-num js-line-number" data-line-number="333"></td> | |
2102 <td id="LC333" class="blob-code blob-code-inner js-file-line"> | |
2103 </td> | |
2104 </tr> | |
2105 <tr> | |
2106 <td id="L334" class="blob-num js-line-number" data-line-number="334"></td> | |
2107 <td id="LC334" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> s <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>, <span class="pl-c1">len</span>(labelList)):</td> | |
2108 </tr> | |
2109 <tr> | |
2110 <td id="L335" class="blob-num js-line-number" data-line-number="335"></td> | |
2111 <td id="LC335" class="blob-code blob-code-inner js-file-line"> ax.barh(ind, composite_df[labelList[s]], width, <span class="pl-v">color</span><span class="pl-k">=</span>palette[s], <span class="pl-v">label</span><span class="pl-k">=</span>labelList[s])</td> | |
2112 </tr> | |
2113 <tr> | |
2114 <td id="L336" class="blob-num js-line-number" data-line-number="336"></td> | |
2115 <td id="LC336" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> ind <span class="pl-k">+</span> width</td> | |
2116 </tr> | |
2117 <tr> | |
2118 <td id="L337" class="blob-num js-line-number" data-line-number="337"></td> | |
2119 <td id="LC337" class="blob-code blob-code-inner js-file-line"> | |
2120 </td> | |
2121 </tr> | |
2122 <tr> | |
2123 <td id="L338" class="blob-num js-line-number" data-line-number="338"></td> | |
2124 <td id="LC338" class="blob-code blob-code-inner js-file-line"> ax.set(<span class="pl-v">yticks</span><span class="pl-k">=</span>np.arange(width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">2</span>)<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>)), <span class="pl-v">yticklabels</span><span class="pl-k">=</span>composite_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span> , ylim=[(len(labelList)-1) * width - 1, len(composite_df)])</span></td> | |
2125 </tr> | |
2126 <tr> | |
2127 <td id="L339" class="blob-num js-line-number" data-line-number="339"></td> | |
2128 <td id="LC339" class="blob-code blob-code-inner js-file-line"> ax.legend()</td> | |
2129 </tr> | |
2130 <tr> | |
2131 <td id="L340" class="blob-num js-line-number" data-line-number="340"></td> | |
2132 <td id="LC340" class="blob-code blob-code-inner js-file-line"> | |
2133 </td> | |
2134 </tr> | |
2135 <tr> | |
2136 <td id="L341" class="blob-num js-line-number" data-line-number="341"></td> | |
2137 <td id="LC341" class="blob-code blob-code-inner js-file-line"> | |
2138 </td> | |
2139 </tr> | |
2140 <tr> | |
2141 <td id="L342" class="blob-num js-line-number" data-line-number="342"></td> | |
2142 <td id="LC342" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)</td> | |
2143 </tr> | |
2144 <tr> | |
2145 <td id="L343" class="blob-num js-line-number" data-line-number="343"></td> | |
2146 <td id="LC343" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td> | |
2147 </tr> | |
2148 <tr> | |
2149 <td id="L344" class="blob-num js-line-number" data-line-number="344"></td> | |
2150 <td id="LC344" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">'</span>Weighted Phylotype Frequency<span class="pl-pds">'</span></span>)</td> | |
2151 </tr> | |
2152 <tr> | |
2153 <td id="L345" class="blob-num js-line-number" data-line-number="345"></td> | |
2154 <td id="LC345" class="blob-code blob-code-inner js-file-line"> | |
2155 </td> | |
2156 </tr> | |
2157 <tr> | |
2158 <td id="L346" class="blob-num js-line-number" data-line-number="346"></td> | |
2159 <td id="LC346" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va="top", wrap="True")</span></td> | |
2160 </tr> | |
2161 <tr> | |
2162 <td id="L347" class="blob-num js-line-number" data-line-number="347"></td> | |
2163 <td id="LC347" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td> | |
2164 </tr> | |
2165 <tr> | |
2166 <td id="L348" class="blob-num js-line-number" data-line-number="348"></td> | |
2167 <td id="LC348" class="blob-code blob-code-inner js-file-line"> | |
2168 </td> | |
2169 </tr> | |
2170 <tr> | |
2171 <td id="L349" class="blob-num js-line-number" data-line-number="349"></td> | |
2172 <td id="LC349" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.92</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td> | |
2173 </tr> | |
2174 <tr> | |
2175 <td id="L350" class="blob-num js-line-number" data-line-number="350"></td> | |
2176 <td id="LC350" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>True<span class="pl-pds">'</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>left<span class="pl-pds">'</span></span>,)</td> | |
2177 </tr> | |
2178 <tr> | |
2179 <td id="L351" class="blob-num js-line-number" data-line-number="351"></td> | |
2180 <td id="LC351" class="blob-code blob-code-inner js-file-line"> | |
2181 </td> | |
2182 </tr> | |
2183 <tr> | |
2184 <td id="L352" class="blob-num js-line-number" data-line-number="352"></td> | |
2185 <td id="LC352" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png<span class="pl-pds">"</span></span>)</td> | |
2186 </tr> | |
2187 <tr> | |
2188 <td id="L353" class="blob-num js-line-number" data-line-number="353"></td> | |
2189 <td id="LC353" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td> | |
2190 </tr> | |
2191 <tr> | |
2192 <td id="L354" class="blob-num js-line-number" data-line-number="354"></td> | |
2193 <td id="LC354" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>phylotypes.pdf<span class="pl-pds">"</span></span>)</td> | |
2194 </tr> | |
2195 <tr> | |
2196 <td id="L355" class="blob-num js-line-number" data-line-number="355"></td> | |
2197 <td id="LC355" class="blob-code blob-code-inner js-file-line"> plt.show()</td> | |
2198 </tr> | |
2199 <tr> | |
2200 <td id="L356" class="blob-num js-line-number" data-line-number="356"></td> | |
2201 <td id="LC356" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> | |
2202 </tr> | |
2203 <tr> | |
2204 <td id="L357" class="blob-num js-line-number" data-line-number="357"></td> | |
2205 <td id="LC357" class="blob-code blob-code-inner js-file-line"> | |
2206 </td> | |
2207 </tr> | |
2208 <tr> | |
2209 <td id="L358" class="blob-num js-line-number" data-line-number="358"></td> | |
2210 <td id="LC358" class="blob-code blob-code-inner js-file-line"> | |
2211 </td> | |
2212 </tr> | |
2213 <tr> | |
2214 <td id="L359" class="blob-num js-line-number" data-line-number="359"></td> | |
2215 <td id="LC359" class="blob-code blob-code-inner js-file-line"> | |
2216 </td> | |
2217 </tr> | |
2218 <tr> | |
2219 <td id="L360" class="blob-num js-line-number" data-line-number="360"></td> | |
2220 <td id="LC360" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">sum2_df</span>):</td> | |
2221 </tr> | |
2222 <tr> | |
2223 <td id="L361" class="blob-num js-line-number" data-line-number="361"></td> | |
2224 <td id="LC361" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab20<span class="pl-pds">'</span></span>)</td> | |
2225 </tr> | |
2226 <tr> | |
2227 <td id="L362" class="blob-num js-line-number" data-line-number="362"></td> | |
2228 <td id="LC362" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td> | |
2229 </tr> | |
2230 <tr> | |
2231 <td id="L363" class="blob-num js-line-number" data-line-number="363"></td> | |
2232 <td id="LC363" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptome. <span class="pl-pds">"</span></span> \</td> | |
2233 </tr> | |
2234 <tr> | |
2235 <td id="L364" class="blob-num js-line-number" data-line-number="364"></td> | |
2236 <td id="LC364" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">"</span></span> \</td> | |
2237 </tr> | |
2238 <tr> | |
2239 <td id="L365" class="blob-num js-line-number" data-line-number="365"></td> | |
2240 <td id="LC365" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>for combined transcript abundance. <span class="pl-pds">"</span></span> \</td> | |
2241 </tr> | |
2242 <tr> | |
2243 <td id="L366" class="blob-num js-line-number" data-line-number="366"></td> | |
2244 <td id="LC366" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> | |
2245 </tr> | |
2246 <tr> | |
2247 <td id="L367" class="blob-num js-line-number" data-line-number="367"></td> | |
2248 <td id="LC367" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get a list of phylotype, create equivalent of saccver, get a list of</span></td> | |
2249 </tr> | |
2250 <tr> | |
2251 <td id="L368" class="blob-num js-line-number" data-line-number="368"></td> | |
2252 <td id="LC368" class="blob-code blob-code-inner js-file-line"> maxFPKM <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].max()</td> | |
2253 </tr> | |
2254 <tr> | |
2255 <td id="L369" class="blob-num js-line-number" data-line-number="369"></td> | |
2256 <td id="LC369" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum()</td> | |
2257 </tr> | |
2258 <tr> | |
2259 <td id="L370" class="blob-num js-line-number" data-line-number="370"></td> | |
2260 <td id="LC370" class="blob-code blob-code-inner js-file-line"> | |
2261 </td> | |
2262 </tr> | |
2263 <tr> | |
2264 <td id="L371" class="blob-num js-line-number" data-line-number="371"></td> | |
2265 <td id="LC371" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Normalised<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], maxFPKM),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> | |
2266 </tr> | |
2267 <tr> | |
2268 <td id="L372" class="blob-num js-line-number" data-line-number="372"></td> | |
2269 <td id="LC372" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Weighted<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], total),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> | |
2270 </tr> | |
2271 <tr> | |
2272 <td id="L373" class="blob-num js-line-number" data-line-number="373"></td> | |
2273 <td id="LC373" class="blob-code blob-code-inner js-file-line"> pList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> | |
2274 </tr> | |
2275 <tr> | |
2276 <td id="L374" class="blob-num js-line-number" data-line-number="374"></td> | |
2277 <td id="LC374" class="blob-code blob-code-inner js-file-line"> phList <span class="pl-k">=</span> []</td> | |
2278 </tr> | |
2279 <tr> | |
2280 <td id="L375" class="blob-num js-line-number" data-line-number="375"></td> | |
2281 <td id="LC375" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pList:</td> | |
2282 </tr> | |
2283 <tr> | |
2284 <td id="L376" class="blob-num js-line-number" data-line-number="376"></td> | |
2285 <td id="LC376" class="blob-code blob-code-inner js-file-line"> phList.append(<span class="pl-c1">str</span>(p))</td> | |
2286 </tr> | |
2287 <tr> | |
2288 <td id="L377" class="blob-num js-line-number" data-line-number="377"></td> | |
2289 <td id="LC377" class="blob-code blob-code-inner js-file-line"> | |
2290 </td> | |
2291 </tr> | |
2292 <tr> | |
2293 <td id="L378" class="blob-num js-line-number" data-line-number="378"></td> | |
2294 <td id="LC378" class="blob-code blob-code-inner js-file-line"> fList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Weighted<span class="pl-pds">'</span></span>]</td> | |
2295 </tr> | |
2296 <tr> | |
2297 <td id="L379" class="blob-num js-line-number" data-line-number="379"></td> | |
2298 <td id="LC379" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(phList)<span class="pl-k">*</span><span class="pl-c1">0.3</span></td> | |
2299 </tr> | |
2300 <tr> | |
2301 <td id="L380" class="blob-num js-line-number" data-line-number="380"></td> | |
2302 <td id="LC380" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td> | |
2303 </tr> | |
2304 <tr> | |
2305 <td id="L381" class="blob-num js-line-number" data-line-number="381"></td> | |
2306 <td id="LC381" class="blob-code blob-code-inner js-file-line"> | |
2307 </td> | |
2308 </tr> | |
2309 <tr> | |
2310 <td id="L382" class="blob-num js-line-number" data-line-number="382"></td> | |
2311 <td id="LC382" class="blob-code blob-code-inner js-file-line"> ax.barh(phList, fList, <span class="pl-v">color</span><span class="pl-k">=</span>palette)</td> | |
2312 </tr> | |
2313 <tr> | |
2314 <td id="L383" class="blob-num js-line-number" data-line-number="383"></td> | |
2315 <td id="LC383" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)</td> | |
2316 </tr> | |
2317 <tr> | |
2318 <td id="L384" class="blob-num js-line-number" data-line-number="384"></td> | |
2319 <td id="LC384" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td> | |
2320 </tr> | |
2321 <tr> | |
2322 <td id="L385" class="blob-num js-line-number" data-line-number="385"></td> | |
2323 <td id="LC385" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">'</span>Weighted Phylotype Frequency<span class="pl-pds">'</span></span>)</td> | |
2324 </tr> | |
2325 <tr> | |
2326 <td id="L386" class="blob-num js-line-number" data-line-number="386"></td> | |
2327 <td id="LC386" class="blob-code blob-code-inner js-file-line"> | |
2328 </td> | |
2329 </tr> | |
2330 <tr> | |
2331 <td id="L387" class="blob-num js-line-number" data-line-number="387"></td> | |
2332 <td id="LC387" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va="top", wrap="True")</span></td> | |
2333 </tr> | |
2334 <tr> | |
2335 <td id="L388" class="blob-num js-line-number" data-line-number="388"></td> | |
2336 <td id="LC388" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td> | |
2337 </tr> | |
2338 <tr> | |
2339 <td id="L389" class="blob-num js-line-number" data-line-number="389"></td> | |
2340 <td id="LC389" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td> | |
2341 </tr> | |
2342 <tr> | |
2343 <td id="L390" class="blob-num js-line-number" data-line-number="390"></td> | |
2344 <td id="LC390" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>True<span class="pl-pds">'</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>left<span class="pl-pds">'</span></span>,)</td> | |
2345 </tr> | |
2346 <tr> | |
2347 <td id="L391" class="blob-num js-line-number" data-line-number="391"></td> | |
2348 <td id="LC391" class="blob-code blob-code-inner js-file-line"> | |
2349 </td> | |
2350 </tr> | |
2351 <tr> | |
2352 <td id="L392" class="blob-num js-line-number" data-line-number="392"></td> | |
2353 <td id="LC392" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png<span class="pl-pds">"</span></span>)</td> | |
2354 </tr> | |
2355 <tr> | |
2356 <td id="L393" class="blob-num js-line-number" data-line-number="393"></td> | |
2357 <td id="LC393" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td> | |
2358 </tr> | |
2359 <tr> | |
2360 <td id="L394" class="blob-num js-line-number" data-line-number="394"></td> | |
2361 <td id="LC394" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>phylotypes.pdf<span class="pl-pds">"</span></span>)</td> | |
2362 </tr> | |
2363 <tr> | |
2364 <td id="L395" class="blob-num js-line-number" data-line-number="395"></td> | |
2365 <td id="LC395" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.show()</span></td> | |
2366 </tr> | |
2367 <tr> | |
2368 <td id="L396" class="blob-num js-line-number" data-line-number="396"></td> | |
2369 <td id="LC396" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> | |
2370 </tr> | |
2371 <tr> | |
2372 <td id="L397" class="blob-num js-line-number" data-line-number="397"></td> | |
2373 <td id="LC397" class="blob-code blob-code-inner js-file-line"> | |
2374 </td> | |
2375 </tr> | |
2376 <tr> | |
2377 <td id="L398" class="blob-num js-line-number" data-line-number="398"></td> | |
2378 <td id="LC398" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}</span></td> | |
2379 </tr> | |
2380 <tr> | |
2381 <td id="L399" class="blob-num js-line-number" data-line-number="399"></td> | |
2382 <td id="LC399" class="blob-code blob-code-inner js-file-line"> | |
2383 </td> | |
2384 </tr> | |
2385 <tr> | |
2386 <td id="L400" class="blob-num js-line-number" data-line-number="400"></td> | |
2387 <td id="LC400" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptomicProcess</span>(<span class="pl-smi">args</span>,<span class="pl-smi">argdict</span>):</td> | |
2388 </tr> | |
2389 <tr> | |
2390 <td id="L401" class="blob-num js-line-number" data-line-number="401"></td> | |
2391 <td id="LC401" class="blob-code blob-code-inner js-file-line"> tdict <span class="pl-k">=</span> {}</td> | |
2392 </tr> | |
2393 <tr> | |
2394 <td id="L402" class="blob-num js-line-number" data-line-number="402"></td> | |
2395 <td id="LC402" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]</td> | |
2396 </tr> | |
2397 <tr> | |
2398 <td id="L403" class="blob-num js-line-number" data-line-number="403"></td> | |
2399 <td id="LC403" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>]]</td> | |
2400 </tr> | |
2401 <tr> | |
2402 <td id="L404" class="blob-num js-line-number" data-line-number="404"></td> | |
2403 <td id="LC404" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>]]</td> | |
2404 </tr> | |
2405 <tr> | |
2406 <td id="L405" class="blob-num js-line-number" data-line-number="405"></td> | |
2407 <td id="LC405" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]]</td> | |
2408 </tr> | |
2409 <tr> | |
2410 <td id="L406" class="blob-num js-line-number" data-line-number="406"></td> | |
2411 <td id="LC406" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>vivax_trans_database<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">'</span></span></td> | |
2412 </tr> | |
2413 <tr> | |
2414 <td id="L407" class="blob-num js-line-number" data-line-number="407"></td> | |
2415 <td id="LC407" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]]</td> | |
2416 </tr> | |
2417 <tr> | |
2418 <td id="L408" class="blob-num js-line-number" data-line-number="408"></td> | |
2419 <td id="LC408" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]]</td> | |
2420 </tr> | |
2421 <tr> | |
2422 <td id="L409" class="blob-num js-line-number" data-line-number="409"></td> | |
2423 <td id="LC409" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]</td> | |
2424 </tr> | |
2425 <tr> | |
2426 <td id="L410" class="blob-num js-line-number" data-line-number="410"></td> | |
2427 <td id="LC410" class="blob-code blob-code-inner js-file-line"> </td> | |
2428 </tr> | |
2429 <tr> | |
2430 <td id="L411" class="blob-num js-line-number" data-line-number="411"></td> | |
2431 <td id="LC411" class="blob-code blob-code-inner js-file-line"> uploadUserReferenceFastq(tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>])</td> | |
2432 </tr> | |
2433 <tr> | |
2434 <td id="L412" class="blob-num js-line-number" data-line-number="412"></td> | |
2435 <td id="LC412" class="blob-code blob-code-inner js-file-line"> transcriptMapping(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses bowtie</span></td> | |
2436 </tr> | |
2437 <tr> | |
2438 <td id="L413" class="blob-num js-line-number" data-line-number="413"></td> | |
2439 <td id="LC413" class="blob-code blob-code-inner js-file-line"> processSamFiles(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses samtools</span></td> | |
2440 </tr> | |
2441 <tr> | |
2442 <td id="L414" class="blob-num js-line-number" data-line-number="414"></td> | |
2443 <td id="LC414" class="blob-code blob-code-inner js-file-line"> transcriptAbundance(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -> ?.cuff/*.*</span></td> | |
2444 </tr> | |
2445 <tr> | |
2446 <td id="L415" class="blob-num js-line-number" data-line-number="415"></td> | |
2447 <td id="LC415" class="blob-code blob-code-inner js-file-line"> transcriptsForBlast(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>creates name+4blast.fa</span></td> | |
2448 </tr> | |
2449 <tr> | |
2450 <td id="L416" class="blob-num js-line-number" data-line-number="416"></td> | |
2451 <td id="LC416" class="blob-code blob-code-inner js-file-line"> blastContigs(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">'</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">'</span></span>)</td> | |
2452 </tr> | |
2453 <tr> | |
2454 <td id="L417" class="blob-num js-line-number" data-line-number="417"></td> | |
2455 <td id="LC417" class="blob-code blob-code-inner js-file-line"> sum_df, sum2_df <span class="pl-k">=</span> combineFPMK(tdict)</td> | |
2456 </tr> | |
2457 <tr> | |
2458 <td id="L418" class="blob-num js-line-number" data-line-number="418"></td> | |
2459 <td id="LC418" class="blob-code blob-code-inner js-file-line"> doBarChart(tdict, sum2_df)</td> | |
2460 </tr> | |
2461 <tr> | |
2462 <td id="L419" class="blob-num js-line-number" data-line-number="419"></td> | |
2463 <td id="LC419" class="blob-code blob-code-inner js-file-line"> createHTML(tdict, sum_df)</td> | |
2464 </tr> | |
2465 <tr> | |
2466 <td id="L420" class="blob-num js-line-number" data-line-number="420"></td> | |
2467 <td id="LC420" class="blob-code blob-code-inner js-file-line"> | |
2468 </td> | |
2469 </tr> | |
2470 <tr> | |
2471 <td id="L421" class="blob-num js-line-number" data-line-number="421"></td> | |
2472 <td id="LC421" class="blob-code blob-code-inner js-file-line"> | |
2473 </td> | |
2474 </tr> | |
2475 <tr> | |
2476 <td id="L422" class="blob-num js-line-number" data-line-number="422"></td> | |
2477 <td id="LC422" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>__main__<span class="pl-pds">"</span></span>:</td> | |
2478 </tr> | |
2479 <tr> | |
2480 <td id="L423" class="blob-num js-line-number" data-line-number="423"></td> | |
2481 <td id="LC423" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">exit</span>()</td> | |
2482 </tr> | |
2483 <tr> | |
2484 <td id="L424" class="blob-num js-line-number" data-line-number="424"></td> | |
2485 <td id="LC424" class="blob-code blob-code-inner js-file-line"> | |
2486 </td> | |
2487 </tr> | |
2488 <tr> | |
2489 <td id="L425" class="blob-num js-line-number" data-line-number="425"></td> | |
2490 <td id="LC425" class="blob-code blob-code-inner js-file-line"> | |
2491 </td> | |
2492 </tr> | |
2493 </table> | |
2494 | |
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2570 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> | |
2571 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> | |
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2577 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script> | |
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2586 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg> | |
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2589 </div> | |
2590 <template id="site-details-dialog"> | |
2591 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open> | |
2592 <summary role="button" aria-label="Close dialog"></summary> | |
2593 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal"> | |
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