Mercurial > repos > johnheap > vapper
comparison Vap.py @ 11:c4463e84a7ea draft
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author | johnheap |
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date | Mon, 03 Jun 2019 14:12:06 -0400 |
parents | 36cb22bd911d |
children | 26ec953069b3 |
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10:6450a72e8f6b | 11:c4463e84a7ea |
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1 """ | 1 |
2 * Copyright 2018 University of Liverpool | 2 |
3 * Author: John Heap, Computational Biology Facility, UoL | 3 |
4 * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL | 4 |
5 * | 5 |
6 * Licensed under the Apache License, Version 2.0 (the "License"); | 6 |
7 * you may not use this file except in compliance with the License. | 7 <!DOCTYPE html> |
8 * You may obtain a copy of the License at | 8 <html lang="en"> |
9 * | 9 <head> |
10 * http://www.apache.org/licenses/LICENSE-2.0 | 10 <meta charset="utf-8"> |
11 * | 11 <link rel="dns-prefetch" href="https://github.githubassets.com"> |
12 * Unless required by applicable law or agreed to in writing, software | 12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> |
13 * distributed under the License is distributed on an "AS IS" BASIS, | 13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> |
14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | 14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> |
15 * See the License for the specific language governing permissions and | 15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> |
16 * limitations under the License. | 16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> |
17 * | 17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> |
18 """ | 18 |
19 #import subprocess | 19 |
20 #import re | 20 |
21 import os | 21 <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" /> |
22 import sys | 22 <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" /> |
23 #import pandas as pd | 23 <link crossorigin="anonymous" media="all" integrity="sha512-XjvAy/mMWN5aOA+pyb/FgAgcVgJkPkwTCwvFK07Ez/H44lvl55ZLGwtpyL4MaMrwDE8QYO+1VYljKFjqr4/iJA==" rel="stylesheet" href="https://github.githubassets.com/assets/github-5b066aa36cc405c9cbcbadf1bde399ed.css" /> |
24 #import numpy as np | 24 |
25 #import seaborn as sns | 25 |
26 #import matplotlib.pyplot as plt | 26 |
27 #from matplotlib.mlab import PCA | 27 |
28 import Tryp_G | 28 |
29 import Tryp_T | 29 <meta name="viewport" content="width=device-width"> |
30 import Tryp_V | 30 |
31 import argparse | 31 <title>VAPPER-Galaxy/Vap.py at master · johnheap/VAPPER-Galaxy · GitHub</title> |
32 #Entry .sort out the arguments | 32 <meta name="description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub."> |
33 | 33 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> |
34 pdfExport = False | 34 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> |
35 #parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.') | 35 <meta property="fb:app_id" content="1401488693436528"> |
36 #parser.add_argument('name') | 36 |
37 #parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway") | 37 <meta name="twitter:image:src" content="https://avatars0.githubusercontent.com/u/24318980?s=400&v=4" /><meta name="twitter:site" content="@github" /><meta name="twitter:card" content="summary" /><meta name="twitter:title" content="johnheap/VAPPER-Galaxy" /><meta name="twitter:description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub." /> |
38 #parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory") | 38 <meta property="og:image" content="https://avatars0.githubusercontent.com/u/24318980?s=400&v=4" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="johnheap/VAPPER-Galaxy" /><meta property="og:url" content="https://github.com/johnheap/VAPPER-Galaxy" /><meta property="og:description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub." /> |
39 #parser.add_argument('strain') | 39 |
40 #parser.add_argument('Forward_Read_File') | 40 <link rel="assets" href="https://github.githubassets.com/"> |
41 #parser.add_argument('Reverse_Read_File') | 41 |
42 #parser.add_argument('htmlfile') | 42 <meta name="pjax-timeout" content="1000"> |
43 #parser.add_argument('htmlresource') | 43 |
44 #parser.add_argument('heatmapFile') | 44 <meta name="request-id" content="99F4:18E6:6FD3A:CCBBE:5CF562F5" data-pjax-transient> |
45 #parser.add_argument('PCAFile') | 45 |
46 #parser.add_argument('devheatmapFile') | 46 |
47 #args = parser.parse_args() | 47 |
48 | 48 |
49 #we have numerous parameters.... | 49 <meta name="selected-link" value="repo_source" data-pjax-transient> |
50 #hard code it for differnt types? | 50 |
51 | 51 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> |
52 | 52 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> |
53 arguments = sys.argv | 53 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc"> |
54 htmldir = arguments[len(arguments)-1] #last argument is always html_resource | 54 |
55 if not os.path.exists(htmldir): | 55 <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="99F4:18E6:6FD3A:CCBBE:5CF562F5" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" /> |
56 os.mkdir(htmldir) | 56 <meta name="analytics-location" content="/<user-name>/<repo-name>/blob/show" data-pjax-transient="true" /> |
57 | 57 |
58 if arguments[1] == 'g_assemble': | 58 |
59 argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10} | 59 |
60 Tryp_G.assemble(arguments,argdict) | 60 <meta name="google-analytics" content="UA-3769691-2"> |
61 if arguments[1] == 'g_contigs': | 61 |
62 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6} | 62 |
63 Tryp_G.contigs(arguments,argdict) | 63 <meta class="js-ga-set" name="dimension1" content="Logged Out"> |
64 if arguments[1] == 'transcipt': | 64 |
65 argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} | 65 |
66 Tryp_T.transcriptomicProcess(arguments,argdict) | 66 |
67 if arguments[1] == 'v_assemble': | 67 |
68 argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10} | 68 |
69 Tryp_V.vivax_assemble(arguments,argdict) | 69 <meta name="hostname" content="github.com"> |
70 if arguments[1] == 'v_contigs': | 70 <meta name="user-login" content=""> |
71 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6} | 71 |
72 Tryp_V.vivax_contigs(arguments,argdict) | 72 <meta name="expected-hostname" content="github.com"> |
73 | 73 <meta name="js-proxy-site-detection-payload" content="NWEwZTMxMzAxNDY4Y2M3ZDk4MDYwMDQwYjA0ZTlhMTY5NTlhZjEyM2Q0ZDIzNTNkYTUwZjk2OTg3OGNjZDI3M3x7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiI5OUY0OjE4RTY6NkZEM0E6Q0NCQkU6NUNGNTYyRjUiLCJ0aW1lc3RhbXAiOjE1NTk1ODU1MjUsImhvc3QiOiJnaXRodWIuY29tIn0="> |
74 | 74 |
75 sys.exit() | 75 <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS"> |
76 | 76 |
77 | 77 <meta name="html-safe-nonce" content="aabe579aff0ce6af1f02bfefa7de34b517b192e3"> |
78 | 78 |
79 #if not os.path.exists(args.htmlresource): | 79 <meta http-equiv="x-pjax-version" content="af1499c2254d0582d0a98af1dfd7f11b"> |
80 # os.mkdir(args.htmlresource) | 80 |
81 #if args.p: | 81 |
82 # pdfExport = True | 82 <link href="https://github.com/johnheap/VAPPER-Galaxy/commits/master.atom" rel="alternate" title="Recent Commits to VAPPER-Galaxy:master" type="application/atom+xml"> |
83 #if args.t: | 83 |
84 # print ("Transcriptomic Pathway") | 84 <meta name="go-import" content="github.com/johnheap/VAPPER-Galaxy git https://github.com/johnheap/VAPPER-Galaxy.git"> |
85 # Tryp_T.transcriptomicProcess(args.name, pdfExport, args.strain, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource) | 85 |
86 #else: | 86 <meta name="octolytics-dimension-user_id" content="24318980" /><meta name="octolytics-dimension-user_login" content="johnheap" /><meta name="octolytics-dimension-repository_id" content="139730674" /><meta name="octolytics-dimension-repository_nwo" content="johnheap/VAPPER-Galaxy" /><meta name="octolytics-dimension-repository_public" content="true" /><meta name="octolytics-dimension-repository_is_fork" content="false" /><meta name="octolytics-dimension-repository_network_root_id" content="139730674" /><meta name="octolytics-dimension-repository_network_root_nwo" content="johnheap/VAPPER-Galaxy" /><meta name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" content="false" /> |
87 #print ('Genomic Pathway') | 87 |
88 #Tryp_G.test_output(args.name, args.htmlfile, args.htmlresource, args.heatmapFile, args.PCAFile,args.devheatmapFile) | 88 |
89 # Tryp_G.genomicProcess(args.name, pdfExport, args.Forward_Read_File, args.Reverse_Read_File, args.htmlfile, args.htmlresource) | 89 <link rel="canonical" href="https://github.com/johnheap/VAPPER-Galaxy/blob/master/Vap.py" data-pjax-transient> |
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204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn & contribute</h4> | |
205 <ul class="list-style-none mb-3"> | |
206 <li class="edge-item-fix"><a href="/topics" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Topics">Topics</a></li> | |
207 <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li> | |
208 <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li> | |
209 <li class="edge-item-fix"><a href="https://lab.github.com/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Learning lab">Learning Lab</a></li> | |
210 <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li> | |
211 </ul> | |
212 | |
213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4> | |
214 <ul class="list-style-none mb-0"> | |
215 <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li> | |
216 <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li> | |
217 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li> | |
218 </ul> | |
219 </div> | |
220 </details> | |
221 </li> | |
222 | |
223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> | |
224 <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a> | |
225 </li> | |
226 | |
227 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> | |
228 <details class="HeaderMenu-details details-overlay details-reset width-full"> | |
229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> | |
230 Pricing | |
231 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> | |
232 <path d="M1,1l6.2,6L13,1"></path> | |
233 </svg> | |
234 </summary> | |
235 | |
236 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> | |
237 <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a> | |
238 | |
239 <ul class="list-style-none mb-3"> | |
240 <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li> | |
241 <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li> | |
242 </ul> | |
243 | |
244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> | |
245 <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> | |
246 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> | |
247 </ul> | |
248 </div> | |
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"> | |
255 <div class="d-lg-flex mb-3 mb-lg-0"> | |
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 > | |
263 <div class="position-relative"> | |
264 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="139730674" data-scoped-search-url="/johnheap/VAPPER-Galaxy/search" data-unscoped-search-url="/search" action="/johnheap/VAPPER-Galaxy/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> | |
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"> | |
266 <input type="text" | |
267 class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable" | |
268 data-hotkey="s,/" | |
269 name="q" | |
270 value="" | |
271 placeholder="Search" | |
272 data-unscoped-placeholder="Search GitHub" | |
273 data-scoped-placeholder="Search" | |
274 autocapitalize="off" | |
275 aria-autocomplete="list" | |
276 aria-controls="jump-to-results" | |
277 aria-label="Search" | |
278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=5MzQ1RlnTKXgRukE3fvG6coUoC2g7caP2Y7AEhL1aj7jsO5luTpWqHOrjoWoNlAo1ormLPudsQBeevTJJMYJwQ==" | |
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"> | |
284 | |
285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> | |
286 | |
287 <ul class="d-none js-jump-to-suggestions-template-container"> | |
288 | |
289 | |
290 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> | |
291 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> | |
292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> | |
293 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> | |
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> | |
296 </div> | |
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"> | |
299 | |
300 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> | |
301 </div> | |
302 | |
303 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> | |
304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> | |
305 In this repository | |
306 </span> | |
307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> | |
308 All GitHub | |
309 </span> | |
310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> | |
311 </div> | |
312 | |
313 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> | |
314 Jump to | |
315 <span class="d-inline-block ml-1 v-align-middle">↵</span> | |
316 </div> | |
317 </a> | |
318 </li> | |
319 | |
320 </ul> | |
321 | |
322 <ul class="d-none js-jump-to-no-results-template-container"> | |
323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> | |
324 <span class="text-gray">No suggested jump to results</span> | |
325 </li> | |
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"> | |
329 | |
330 | |
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"> | |
332 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> | |
333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> | |
334 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> | |
335 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> | |
336 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> | |
337 </div> | |
338 | |
339 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> | |
340 | |
341 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> | |
342 </div> | |
343 | |
344 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> | |
345 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> | |
346 In this repository | |
347 </span> | |
348 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> | |
349 All GitHub | |
350 </span> | |
351 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> | |
352 </div> | |
353 | |
354 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> | |
355 Jump to | |
356 <span class="d-inline-block ml-1 v-align-middle">↵</span> | |
357 </div> | |
358 </a> | |
359 </li> | |
360 | |
361 | |
362 | |
363 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option"> | |
364 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> | |
365 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> | |
366 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> | |
367 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> | |
368 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> | |
369 </div> | |
370 | |
371 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> | |
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":"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"> | |
404 Sign in | |
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":"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"> | |
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 | |
441 | |
442 | |
443 | |
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":"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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708 <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> | |
709 </button> | |
710 </div> | |
711 </div> | |
712 </div> | |
713 | |
714 | |
715 | |
716 <div itemprop="text" class="Box-body p-0 blob-wrapper data type-python "> | |
717 | |
718 <table class="highlight tab-size js-file-line-container" data-tab-size="8"> | |
719 <tr> | |
720 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> | |
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"> * Copyright 2018 University of Liverpool</span></td> | |
726 </tr> | |
727 <tr> | |
728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> | |
729 <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author: John Heap, Computational Biology Facility, UoL</span></td> | |
730 </tr> | |
731 <tr> | |
732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> | |
733 <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td> | |
734 </tr> | |
735 <tr> | |
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"> *</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"> * Licensed under the Apache License, Version 2.0 (the "License");</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"> * you may not use this file except in compliance with the License.</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"> * You may obtain a copy of the License at</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"> *</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"> * http://www.apache.org/licenses/LICENSE-2.0</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"> * Unless required by applicable law or agreed to in writing, software</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"> * distributed under the License is distributed on an "AS IS" BASIS,</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"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</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"> * See the License for the specific language governing permissions and</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"> * limitations under the License.</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"> *</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"> <span class="pl-pds">"""</span></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-c"><span class="pl-c">#</span>import subprocess</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-c"><span class="pl-c">#</span>import re</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"><span class="pl-k">import</span> os</td> | |
802 </tr> | |
803 <tr> | |
804 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> | |
805 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td> | |
806 </tr> | |
807 <tr> | |
808 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> | |
809 <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> | |
810 </tr> | |
811 <tr> | |
812 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> | |
813 <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> | |
814 </tr> | |
815 <tr> | |
816 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> | |
817 <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> | |
818 </tr> | |
819 <tr> | |
820 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> | |
821 <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> | |
822 </tr> | |
823 <tr> | |
824 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> | |
825 <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> | |
826 </tr> | |
827 <tr> | |
828 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> | |
829 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_G</td> | |
830 </tr> | |
831 <tr> | |
832 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> | |
833 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_T</td> | |
834 </tr> | |
835 <tr> | |
836 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> | |
837 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V</td> | |
838 </tr> | |
839 <tr> | |
840 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> | |
841 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V_T</td> | |
842 </tr> | |
843 <tr> | |
844 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> | |
845 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> argparse</td> | |
846 </tr> | |
847 <tr> | |
848 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> | |
849 <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> | |
850 </tr> | |
851 <tr> | |
852 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> | |
853 <td id="LC34" class="blob-code blob-code-inner js-file-line"> | |
854 </td> | |
855 </tr> | |
856 <tr> | |
857 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> | |
858 <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> | |
859 </tr> | |
860 <tr> | |
861 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> | |
862 <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> | |
863 </tr> | |
864 <tr> | |
865 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> | |
866 <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> | |
867 </tr> | |
868 <tr> | |
869 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> | |
870 <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> | |
871 </tr> | |
872 <tr> | |
873 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> | |
874 <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> | |
875 </tr> | |
876 <tr> | |
877 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> | |
878 <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> | |
879 </tr> | |
880 <tr> | |
881 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> | |
882 <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> | |
883 </tr> | |
884 <tr> | |
885 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> | |
886 <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> | |
887 </tr> | |
888 <tr> | |
889 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> | |
890 <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> | |
891 </tr> | |
892 <tr> | |
893 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> | |
894 <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> | |
895 </tr> | |
896 <tr> | |
897 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> | |
898 <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> | |
899 </tr> | |
900 <tr> | |
901 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> | |
902 <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> | |
903 </tr> | |
904 <tr> | |
905 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> | |
906 <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> | |
907 </tr> | |
908 <tr> | |
909 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> | |
910 <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> | |
911 </tr> | |
912 <tr> | |
913 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> | |
914 <td id="LC49" class="blob-code blob-code-inner js-file-line"> | |
915 </td> | |
916 </tr> | |
917 <tr> | |
918 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> | |
919 <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> | |
920 </tr> | |
921 <tr> | |
922 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> | |
923 <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> | |
924 </tr> | |
925 <tr> | |
926 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> | |
927 <td id="LC52" class="blob-code blob-code-inner js-file-line"> | |
928 </td> | |
929 </tr> | |
930 <tr> | |
931 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> | |
932 <td id="LC53" class="blob-code blob-code-inner js-file-line"> | |
933 </td> | |
934 </tr> | |
935 <tr> | |
936 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> | |
937 <td id="LC54" class="blob-code blob-code-inner js-file-line">arguments <span class="pl-k">=</span> sys.argv</td> | |
938 </tr> | |
939 <tr> | |
940 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> | |
941 <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> | |
942 </tr> | |
943 <tr> | |
944 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> | |
945 <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> | |
946 </tr> | |
947 <tr> | |
948 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> | |
949 <td id="LC57" class="blob-code blob-code-inner js-file-line"> os.mkdir(htmldir)</td> | |
950 </tr> | |
951 <tr> | |
952 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> | |
953 <td id="LC58" class="blob-code blob-code-inner js-file-line"> | |
954 </td> | |
955 </tr> | |
956 <tr> | |
957 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> | |
958 <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> | |
959 </tr> | |
960 <tr> | |
961 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> | |
962 <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> | |
963 </tr> | |
964 <tr> | |
965 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> | |
966 <td id="LC61" class="blob-code blob-code-inner js-file-line"> Tryp_G.assemble(arguments,argdict)</td> | |
967 </tr> | |
968 <tr> | |
969 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> | |
970 <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> | |
971 </tr> | |
972 <tr> | |
973 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> | |
974 <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> | |
975 </tr> | |
976 <tr> | |
977 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> | |
978 <td id="LC64" class="blob-code blob-code-inner js-file-line"> Tryp_G.contigs(arguments,argdict)</td> | |
979 </tr> | |
980 <tr> | |
981 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> | |
982 <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> | |
983 </tr> | |
984 <tr> | |
985 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> | |
986 <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> | |
987 </tr> | |
988 <tr> | |
989 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> | |
990 <td id="LC67" class="blob-code blob-code-inner js-file-line"> Tryp_T.transcriptomicProcess(arguments,argdict)</td> | |
991 </tr> | |
992 <tr> | |
993 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> | |
994 <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> | |
995 </tr> | |
996 <tr> | |
997 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> | |
998 <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> | |
999 </tr> | |
1000 <tr> | |
1001 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> | |
1002 <td id="LC70" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_assemble(arguments,argdict)</td> | |
1003 </tr> | |
1004 <tr> | |
1005 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> | |
1006 <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> | |
1007 </tr> | |
1008 <tr> | |
1009 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> | |
1010 <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> | |
1011 </tr> | |
1012 <tr> | |
1013 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> | |
1014 <td id="LC73" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_contigs(arguments,argdict)</td> | |
1015 </tr> | |
1016 <tr> | |
1017 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> | |
1018 <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> | |
1019 </tr> | |
1020 <tr> | |
1021 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> | |
1022 <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> | |
1023 </tr> | |
1024 <tr> | |
1025 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> | |
1026 <td id="LC76" class="blob-code blob-code-inner js-file-line"> Tryp_V_T.transcriptomicProcess(arguments,argdict)</td> | |
1027 </tr> | |
1028 <tr> | |
1029 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> | |
1030 <td id="LC77" class="blob-code blob-code-inner js-file-line"> | |
1031 </td> | |
1032 </tr> | |
1033 <tr> | |
1034 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> | |
1035 <td id="LC78" class="blob-code blob-code-inner js-file-line"> | |
1036 </td> | |
1037 </tr> | |
1038 <tr> | |
1039 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> | |
1040 <td id="LC79" class="blob-code blob-code-inner js-file-line">sys.exit()</td> | |
1041 </tr> | |
1042 <tr> | |
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1044 <td id="LC80" class="blob-code blob-code-inner js-file-line"> | |
1045 </td> | |
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