Mercurial > repos > johnheap > vapper
changeset 20:26ec953069b3 draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 16:02:02 -0400 |
| parents | fe79425b1fa4 |
| children | 1b5bf8383973 |
| files | Vap.py |
| diffstat | 1 files changed, 72 insertions(+), 1157 deletions(-) [+] |
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<label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container"> - <input type="text" - class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable" - data-hotkey="s,/" - name="q" - value="" - placeholder="Search" - data-unscoped-placeholder="Search GitHub" - data-scoped-placeholder="Search" - autocapitalize="off" - aria-autocomplete="list" - aria-controls="jump-to-results" - aria-label="Search" - data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=5MzQ1RlnTKXgRukE3fvG6coUoC2g7caP2Y7AEhL1aj7jsO5luTpWqHOrjoWoNlAo1ormLPudsQBeevTJJMYJwQ==" - spellcheck="false" - autocomplete="off" - > - <input type="hidden" class="js-site-search-type-field" name="type" > - <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> +""" + * Copyright 2018 University of Liverpool + * Author: John Heap, Computational Biology Facility, UoL + * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + """ +#import subprocess +#import re +import os +import sys +#import pandas as pd +#import numpy as np +#import seaborn as sns +#import matplotlib.pyplot as plt +#from matplotlib.mlab import PCA +import Tryp_G +import Tryp_T +import Tryp_V +import Tryp_V_T +import argparse +#Entry .sort out the arguments - <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> - -<ul class="d-none js-jump-to-suggestions-template-container"> - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - 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In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - -</ul> - -<ul class="d-none js-jump-to-no-results-template-container"> - <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> - <span class="text-gray">No suggested jump to results</span> - </li> -</ul> - -<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"> - - -<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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<svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - 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Sign in -</a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"99F4:18E6:6FD3A:CCBBE:5CF562F5","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Vap.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="61d34ac29eda53a9af41882fb756e16915c4f2c290c4b6305a2d6e690cf24bbf" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo"> - Sign up -</a> </div> - </div> - </div> -</header> - - </div> - - <div id="start-of-content" class="show-on-focus"></div> - - - <div id="js-flash-container"> - -</div> - - - - <div class="application-main " data-commit-hovercards-enabled> - <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> - <main > - - +pdfExport = False +#parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.') +#parser.add_argument('name') +#parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway") +#parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory") +#parser.add_argument('strain') +#parser.add_argument('Forward_Read_File') +#parser.add_argument('Reverse_Read_File') +#parser.add_argument('htmlfile') +#parser.add_argument('htmlresource') +#parser.add_argument('heatmapFile') +#parser.add_argument('PCAFile') +#parser.add_argument('devheatmapFile') +#args = parser.parse_args() - - - - - - - - <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav pt-0 pt-lg-4 "> - <div class="repohead-details-container clearfix container-lg p-responsive d-none d-lg-block"> - - <ul class="pagehead-actions"> - - - - - <li> - - <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":"99F4:18E6:6FD3A:CCBBE:5CF562F5","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Vap.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="70fbddf86f10bcc009cd363c7eb93ed0fce302ed45b779d8040d24c73dea92f6" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy"> - 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</include-fragment> - </details-menu> -</details> +arguments = sys.argv +htmldir = arguments[len(arguments)-1] #last argument is always html_resource +if not os.path.exists(htmldir): + os.mkdir(htmldir) - <div class="BtnGroup flex-shrink-0 d-md-none"> - <a href="/johnheap/VAPPER-Galaxy/find/master" - class="js-pjax-capture-input btn btn-sm BtnGroup-item" - data-pjax - data-hotkey="t"> - Find file - </a> - <clipboard-copy value="Vap.py" class="btn btn-sm BtnGroup-item"> - Copy path - </clipboard-copy> - </div> - </span> - <h2 id="blob-path" class="breadcrumb flex-auto min-width-0 text-normal flex-md-self-center ml-md-2 mr-md-3 my-2 my-md-0"> - <span class="js-repo-root text-bold"><span class="js-path-segment"><a data-pjax="true" href="/johnheap/VAPPER-Galaxy"><span>VAPPER-Galaxy</span></a></span></span><span class="separator">/</span><strong class="final-path">Vap.py</strong> - </h2> - - <div class="BtnGroup flex-shrink-0 d-none d-md-inline-block"> - <a href="/johnheap/VAPPER-Galaxy/find/master" - class="js-pjax-capture-input btn btn-sm BtnGroup-item" - data-pjax - data-hotkey="t"> - Find file - </a> - <clipboard-copy value="Vap.py" class="btn btn-sm BtnGroup-item"> - Copy path - </clipboard-copy> - </div> - </div> - - - - <include-fragment src="/johnheap/VAPPER-Galaxy/contributors/master/Vap.py" class="Box Box--condensed commit-loader"> - <div class="Box-body bg-blue-light f6"> - Fetching contributors… - </div> - - <div class="Box-body d-flex flex-items-center" > - <img alt="" class="loader-loading mr-2" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" /> - <span class="text-red h6 loader-error">Cannot retrieve contributors at this time</span> - </div> -</include-fragment> - - - - - - <div class="Box mt-3 position-relative"> - -<div class="Box-header py-2 d-flex flex-column flex-shrink-0 flex-md-row flex-md-items-center"> - - <div class="text-mono f6 flex-auto pr-3 flex-order-2 flex-md-order-1 mt-2 mt-md-0"> - 81 lines (72 sloc) - <span class="file-info-divider"></span> - 3.04 KB - </div> - - <div class="d-flex py-1 py-md-0 flex-auto flex-order-1 flex-md-order-2 flex-sm-grow-0 flex-justify-between"> - - <div class="BtnGroup"> - <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/raw/master/Vap.py">Raw</a> - <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/johnheap/VAPPER-Galaxy/blame/master/Vap.py">Blame</a> - <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/Vap.py">History</a> - </div> +if arguments[1] == 'g_assemble': + argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10} + Tryp_G.assemble(arguments,argdict) +if arguments[1] == 'g_contigs': + argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6} + Tryp_G.contigs(arguments,argdict) +if arguments[1] == 'transcipt': + argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} + Tryp_T.transcriptomicProcess(arguments,argdict) +if arguments[1] == 'v_assemble': + argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10} + Tryp_V.vivax_assemble(arguments,argdict) +if arguments[1] == 'v_contigs': + argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6} + Tryp_V.vivax_contigs(arguments,argdict) +if arguments[1] == 'v_transcript': + argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} + Tryp_V_T.transcriptomicProcess(arguments,argdict) - <div> - - <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw" - aria-label="You must be signed in to make or propose changes"> - <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg> - </button> - <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw" - aria-label="You must be signed in to make or propose changes"> - <svg class="octicon octicon-trashcan" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg> - </button> - </div> - </div> -</div> - - +sys.exit() - <div itemprop="text" class="Box-body p-0 blob-wrapper data type-python "> - -<table class="highlight tab-size js-file-line-container" data-tab-size="8"> - <tr> - <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> - <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">"""</span></span></td> - </tr> - <tr> - <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> - <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td> - </tr> - <tr> - <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> - <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author: John Heap, Computational Biology Facility, UoL</span></td> - </tr> - <tr> - <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> - <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td> - </tr> - <tr> - <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> - <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> - </tr> - <tr> - <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> - <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the "License");</span></td> - </tr> - <tr> - <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> - <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td> - </tr> - <tr> - <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> - <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td> - </tr> - <tr> - <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> - <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> - </tr> - <tr> - <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> - <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td> - </tr> - <tr> - <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> - <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> - </tr> - <tr> - <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> - <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td> - </tr> - <tr> - <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> - <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td> - </tr> - <tr> - <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> - <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td> - </tr> - <tr> - <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> - <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td> - </tr> - <tr> - <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> - <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td> - </tr> - <tr> - <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> - <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> - </tr> - <tr> - <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> - <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td> - </tr> - <tr> - <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> - <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import subprocess</span></td> - </tr> - <tr> - <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> - <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import re</span></td> - </tr> - <tr> - <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> - <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td> - </tr> - <tr> - <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> - <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td> - </tr> - <tr> - <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> - <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import pandas as pd</span></td> - </tr> - <tr> - <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> - <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import numpy as np</span></td> - </tr> - <tr> - <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> - <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import seaborn as sns</span></td> - </tr> - <tr> - <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> - <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import matplotlib.pyplot as plt</span></td> - </tr> - <tr> - <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> - <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>from matplotlib.mlab import PCA</span></td> - </tr> - <tr> - <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> - <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_G</td> - </tr> - <tr> - <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> - <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_T</td> - </tr> - <tr> - <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> - <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V</td> - </tr> - <tr> - <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> - <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V_T</td> - </tr> - <tr> - <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> - <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> argparse</td> - </tr> - <tr> - <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> - <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>Entry .sort out the arguments</span></td> - </tr> - <tr> - <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> - <td id="LC34" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> - <td id="LC35" class="blob-code blob-code-inner js-file-line">pdfExport <span class="pl-k">=</span> <span class="pl-c1">False</span></td> - </tr> - <tr> - <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> - <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.')</span></td> - </tr> - <tr> - <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> - <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('name')</span></td> - </tr> - <tr> - <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> - <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway")</span></td> - </tr> - <tr> - <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> - <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory")</span></td> - </tr> - <tr> - <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> - <td id="LC40" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('strain')</span></td> - </tr> - <tr> - <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> - <td id="LC41" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('Forward_Read_File')</span></td> - </tr> - <tr> - <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> - <td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('Reverse_Read_File')</span></td> - </tr> - <tr> - <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> - <td id="LC43" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('htmlfile')</span></td> - </tr> - <tr> - <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> - <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('htmlresource')</span></td> - </tr> - <tr> - <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> - <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('heatmapFile')</span></td> - </tr> - <tr> - <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> - <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('PCAFile')</span></td> - </tr> - <tr> - <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> - <td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('devheatmapFile')</span></td> - </tr> - <tr> - <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> - <td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>args = parser.parse_args()</span></td> - </tr> - <tr> - <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> - <td id="LC49" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> - <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>we have numerous parameters....</span></td> - </tr> - <tr> - <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> - <td id="LC51" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>hard code it for differnt types?</span></td> - </tr> - <tr> - <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> - <td id="LC52" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> - <td id="LC53" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> - <td id="LC54" class="blob-code blob-code-inner js-file-line">arguments <span class="pl-k">=</span> sys.argv</td> - </tr> - <tr> - <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> - <td id="LC55" class="blob-code blob-code-inner js-file-line">htmldir <span class="pl-k">=</span> arguments[<span class="pl-c1">len</span>(arguments)<span class="pl-k">-</span><span class="pl-c1">1</span>] <span class="pl-c"><span class="pl-c">#</span>last argument is always html_resource</span></td> - </tr> - <tr> - <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> - <td id="LC56" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-k">not</span> os.path.exists(htmldir):</td> - </tr> - <tr> - <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> - <td id="LC57" class="blob-code blob-code-inner js-file-line"> os.mkdir(htmldir)</td> - </tr> - <tr> - <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> - <td id="LC58" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> - <td id="LC59" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>g_assemble<span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> - <td id="LC60" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>kmers<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>,<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>:<span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>:<span class="pl-c1">8</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">9</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">10</span>}</td> - </tr> - <tr> - <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> - <td id="LC61" class="blob-code blob-code-inner js-file-line"> Tryp_G.assemble(arguments,argdict)</td> - </tr> - <tr> - <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> - <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>g_contigs<span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> - <td id="LC63" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>}</td> - </tr> - <tr> - <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> - <td id="LC64" class="blob-code blob-code-inner js-file-line"> Tryp_G.contigs(arguments,argdict)</td> - </tr> - <tr> - <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> - <td id="LC65" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>transcipt<span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> - <td id="LC66" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>: <span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>: <span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>: <span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>: <span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>: <span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>: <span class="pl-c1">8</span>}</td> - </tr> - <tr> - <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> - <td id="LC67" class="blob-code blob-code-inner js-file-line"> Tryp_T.transcriptomicProcess(arguments,argdict)</td> - </tr> - <tr> - <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> - <td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_assemble<span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> - <td id="LC69" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>kmers<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>,<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>:<span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>:<span class="pl-c1">8</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">9</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">10</span>}</td> - </tr> - <tr> - <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> - <td id="LC70" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_assemble(arguments,argdict)</td> - </tr> - <tr> - <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> - <td id="LC71" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_contigs<span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> - <td id="LC72" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>}</td> - </tr> - <tr> - <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> - <td id="LC73" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_contigs(arguments,argdict)</td> - </tr> - <tr> - <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> - <td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_transcript<span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> - <td id="LC75" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>: <span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>: <span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>: <span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>: <span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>: <span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>: <span class="pl-c1">8</span>}</td> - </tr> - <tr> - <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> - <td id="LC76" class="blob-code blob-code-inner js-file-line"> Tryp_V_T.transcriptomicProcess(arguments,argdict)</td> - </tr> - <tr> - <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> - <td id="LC77" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> - <td id="LC78" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> - <td id="LC79" class="blob-code blob-code-inner js-file-line">sys.exit()</td> - </tr> - <tr> - <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> - <td id="LC80" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> -</table> - - <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true"> - 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