Mercurial > repos > johnheap > vapper
changeset 11:c4463e84a7ea draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 14:12:06 -0400 |
| parents | 6450a72e8f6b |
| children | 491102c84b20 |
| files | Vap.py |
| diffstat | 1 files changed, 1165 insertions(+), 91 deletions(-) [+] |
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--- a/Vap.py Mon Jun 03 14:11:12 2019 -0400 +++ b/Vap.py Mon Jun 03 14:12:06 2019 -0400 @@ -1,91 +1,1165 @@ -""" - * 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 argparse -#Entry .sort out the arguments - -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() - -#we have numerous parameters.... -#hard code it for differnt types? - - -arguments = sys.argv -htmldir = arguments[len(arguments)-1] #last argument is always html_resource -if not os.path.exists(htmldir): - os.mkdir(htmldir) - -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) - - -sys.exit() - - - -#if not os.path.exists(args.htmlresource): -# os.mkdir(args.htmlresource) -#if args.p: -# pdfExport = True -#if args.t: -# print ("Transcriptomic Pathway") -# Tryp_T.transcriptomicProcess(args.name, pdfExport, args.strain, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource) -#else: - #print ('Genomic Pathway') - #Tryp_G.test_output(args.name, args.htmlfile, args.htmlresource, args.heatmapFile, args.PCAFile,args.devheatmapFile) -# Tryp_G.genomicProcess(args.name, pdfExport, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource) - - + + + + + + +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> + <link rel="dns-prefetch" href="https://github.githubassets.com"> + <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> + <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> + <link rel="dns-prefetch" 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Events">Events</a></li> + <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li> + <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li> + </ul> + </div> + </details> + </li> + + <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> + <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a> + </li> + + <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> + <details class="HeaderMenu-details details-overlay details-reset width-full"> + <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> + Pricing + <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> + <path d="M1,1l6.2,6L13,1"></path> + </svg> + </summary> + + <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> + <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a> + + <ul class="list-style-none mb-3"> + <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li> + <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li> + </ul> + + <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> + <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> + <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> + </ul> + </div> + </details> + </li> + </ul> + </nav> + + <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left"> + <div class="d-lg-flex mb-3 mb-lg-0"> + <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" + role="combobox" + aria-owns="jump-to-results" + aria-label="Search or jump to" + aria-haspopup="listbox" + aria-expanded="false" +> + <div class="position-relative"> + <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="139730674" data-scoped-search-url="/johnheap/VAPPER-Galaxy/search" data-unscoped-search-url="/search" action="/johnheap/VAPPER-Galaxy/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> + <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"> + + <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> + +<ul class="d-none js-jump-to-suggestions-template-container"> + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> + <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <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"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> + <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> + <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + +</ul> + + </div> + </label> +</form> </div> +</div> + + </div> + + <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"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="6cb09967fc8eff5df7462c4872e08a94534298b18d1e525416a9c3057ff1d33a" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FVap.py"> + Sign in +</a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header 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 > + + + + + + + + + + + <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}}" 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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"> + <summary class="btn-octicon 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