Mercurial > repos > johnheap > vapper

comparison Tryp_V_T.py @ 9:a0d5e1f5bec0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author johnheap
date Mon, 03 Jun 2019 14:09:49 -0400
parents
children fe79425b1fa4
comparison
equal deleted inserted replaced
8:e75a85590041 9:a0d5e1f5bec0
1
2
3
4
5
6
7 <!DOCTYPE html>
8 <html lang="en">
9 <head>
10 <meta charset="utf-8">
11 <link rel="dns-prefetch" href="https://github.githubassets.com">
12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com">
13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com">
14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com">
15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com">
16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com">
17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/">
18
19
20
21 <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" />
22 <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" />
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
25
26
27
28
29 <meta name="viewport" content="width=device-width">
30
31 <title>VAPPER-Galaxy/Tryp_V_T.py at master · johnheap/VAPPER-Galaxy · GitHub</title>
32 <meta name="description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub.">
33 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
34 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub">
35 <meta property="fb:app_id" content="1401488693436528">
36
37 <meta name="twitter:image:src" content="https://avatars0.githubusercontent.com/u/24318980?s=400&amp;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 <meta property="og:image" content="https://avatars0.githubusercontent.com/u/24318980?s=400&amp;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
40 <link rel="assets" href="https://github.githubassets.com/">
41
42 <meta name="pjax-timeout" content="1000">
43
44 <meta name="request-id" content="A691:31FC:5350A:9C70E:5CF5626C" data-pjax-transient>
45
46
47
48
49 <meta name="selected-link" value="repo_source" data-pjax-transient>
50
51 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU">
52 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA">
53 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc">
54
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="A691:31FC:5350A:9C70E:5CF5626C" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" />
56 <meta name="analytics-location" content="/&lt;user-name&gt;/&lt;repo-name&gt;/blob/show" data-pjax-transient="true" />
57
58
59
60 <meta name="google-analytics" content="UA-3769691-2">
61
62
63 <meta class="js-ga-set" name="dimension1" content="Logged Out">
64
65
66
67
68
69 <meta name="hostname" content="github.com">
70 <meta name="user-login" content="">
71
72 <meta name="expected-hostname" content="github.com">
73 <meta name="js-proxy-site-detection-payload" content="NzYzOGJlZTMwMzU0NWQ4MmU4MGE3MDYxZDI2MDFiZjQxMjBkYTg5NWI1NWRjYzdmZWNjMmE4MWRhZGIxMTMyN3x7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiJBNjkxOjMxRkM6NTM1MEE6OUM3MEU6NUNGNTYyNkMiLCJ0aW1lc3RhbXAiOjE1NTk1ODUzODksImhvc3QiOiJnaXRodWIuY29tIn0=">
74
75 <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS">
76
77 <meta name="html-safe-nonce" content="a37d7307800ea044bd751b0f42a3fd6deab2c7ff">
78
79 <meta http-equiv="x-pjax-version" content="af1499c2254d0582d0a98af1dfd7f11b">
80
81
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
84 <meta name="go-import" content="github.com/johnheap/VAPPER-Galaxy git https://github.com/johnheap/VAPPER-Galaxy.git">
85
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
88
89 <link rel="canonical" href="https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py" data-pjax-transient>
90
91
92 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats">
93
94 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors">
95
96 <link rel="mask-icon" href="https://github.githubassets.com/pinned-octocat.svg" color="#000000">
97 <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://github.githubassets.com/favicon.ico">
98
99 <meta name="theme-color" content="#1e2327">
100
101
102
103
104
105 <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials">
106
107 </head>
108
109 <body class="logged-out env-production page-responsive page-blob">
110
111
112 <div class="position-relative js-header-wrapper ">
113 <a href="#start-of-content" tabindex="1" class="px-2 py-4 bg-blue text-white show-on-focus js-skip-to-content">Skip to content</a>
114 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div>
115
116
117
118
119
120
121 <header class="Header-old header-logged-out js-details-container Details position-relative f4 py-2" role="banner">
122 <div class="container-lg d-lg-flex flex-items-center p-responsive">
123 <div class="d-flex flex-justify-between flex-items-center">
124 <a class="mr-4" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
125 <svg height="32" class="octicon octicon-mark-github text-white" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
126 </a>
127
128 <div class="d-lg-none css-truncate css-truncate-target width-fit p-2">
129
130 <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><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>
131 <a class="Header-link" href="/johnheap">johnheap</a>
132 /
133 <a class="Header-link" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a>
134
135
136 </div>
137
138 <div class="d-flex flex-items-center">
139 <a class="d-inline-block d-lg-none f5 text-white no-underline border border-gray-dark rounded-2 px-2 py-1 mr-3 mr-sm-5" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A691:31FC:5350A:9C70E:5CF5626C&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="dafab2b648ecc3a2244a0de6c85d4884478b192e1ed71d278d79bf55e6dcddd9" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
140 Sign&nbsp;up
141 </a>
142 <button class="btn-link d-lg-none mt-1 js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
143 <svg height="24" class="octicon octicon-three-bars text-white" viewBox="0 0 12 16" version="1.1" width="18" aria-hidden="true"><path fill-rule="evenodd" d="M11.41 9H.59C0 9 0 8.59 0 8c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zm0-4H.59C0 5 0 4.59 0 4c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zM.59 11H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1H.59C0 13 0 12.59 0 12c0-.59 0-1 .59-1z"/></svg>
144 </button>
145 </div>
146 </div>
147
148 <div class="HeaderMenu HeaderMenu--logged-out position-fixed top-0 right-0 bottom-0 height-fit position-lg-relative d-lg-flex flex-justify-between flex-items-center flex-auto">
149 <div class="d-flex d-lg-none flex-justify-end border-bottom bg-gray-light p-3">
150 <button class="btn-link js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
151 <svg height="24" class="octicon octicon-x text-gray" viewBox="0 0 12 16" version="1.1" width="18" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
152 </button>
153 </div>
154
155 <nav class="mt-0 px-3 px-lg-0 mb-5 mb-lg-0" aria-label="Global">
156 <ul class="d-lg-flex list-style-none">
157 <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 ">
158 <details class="HeaderMenu-details details-overlay details-reset width-full">
159 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
160 Why GitHub?
161 <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">
162 <path d="M1,1l6.2,6L13,1"></path>
163 </svg>
164 </summary>
165 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
166 <a href="/features" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Features">Features <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a>
167 <ul class="list-style-none f5 pb-3">
168 <li class="edge-item-fix"><a href="/features/code-review/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code review">Code review</a></li>
169 <li class="edge-item-fix"><a href="/features/project-management/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Project management">Project management</a></li>
170 <li class="edge-item-fix"><a href="/features/integrations" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Integrations">Integrations</a></li>
171 <li class="edge-item-fix"><a href="/features/actions" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Actions">Actions</a>
172 <li class="edge-item-fix"><a href="/features/package-registry" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Package Registry">Package registry</a>
173 <li class="edge-item-fix"><a href="/features#team-management" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Team management">Team management</a></li>
174 <li class="edge-item-fix"><a href="/features#social-coding" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Social coding">Social coding</a></li>
175 <li class="edge-item-fix"><a href="/features#documentation" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Documentation">Documentation</a></li>
176 <li class="edge-item-fix"><a href="/features#code-hosting" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code hosting">Code hosting</a></li>
177 </ul>
178
179 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
180 <li class="edge-item-fix"><a href="/customer-stories" 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 Customer stories">Customer stories <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
181 <li class="edge-item-fix"><a href="/security" 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 Security">Security <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
182 </ul>
183 </div>
184 </details>
185 </li>
186 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
187 <a href="/enterprise" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Enterprise">Enterprise</a>
188 </li>
189
190 <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 ">
191 <details class="HeaderMenu-details details-overlay details-reset width-full">
192 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
193 Explore
194 <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">
195 <path d="M1,1l6.2,6L13,1"></path>
196 </svg>
197 </summary>
198
199 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
200 <ul class="list-style-none mb-3">
201 <li class="edge-item-fix"><a href="/explore" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Explore">Explore GitHub <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
202 </ul>
203
204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn &amp; 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">&rarr;</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">&rarr;</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">&rarr;</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="&#x2713;" />
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=OeWfhCkNlueqmf+vlMZUOIoZL/xaxMnWSzEKmM+a3P/55zFIrfSMdNtX4Lcjm/pZKDqzddz2DGdPMz+4X5/nxg=="
279 spellcheck="false"
280 autocomplete="off"
281 >
282 <input type="hidden" class="js-site-search-type-field" name="type" >
283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
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="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A691:31FC:5350A:9C70E:5CF5626C&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="337eab5a1a33edba9a56afe56b6817bbe2bfb8bfab94836352641826ce53b626" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FTryp_V_T.py">
404 Sign&nbsp;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="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A691:31FC:5350A:9C70E:5CF5626C&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="ae884c1f61e6facf2cb96fcd7d55fbcf227cb7989e192de2cb6c5ab5c46e53d1" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
406 Sign&nbsp;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="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;notification subscription menu watch&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A691:31FC:5350A:9C70E:5CF5626C&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="af7329bf60da95c08a620876666a89de6aa2bf96a8da8486f5eb50741ad8743e" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy">
447 <svg class="octicon octicon-eye v-align-text-bottom" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg>
448 Watch
449 </a> <a class="social-count" href="/johnheap/VAPPER-Galaxy/watchers"
450 aria-label="0 users are watching this repository">
451 0
452 </a>
453
454 </li>
455
456 <li>
457 <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to star a repository" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;star button&quot;,&quot;repository_id&quot;:139730674,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A691:31FC:5350A:9C70E:5CF5626C&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="0db565041ee36ff7a0a3ca6a8ab0c55e0708db9b7f32415674420a32f9615882" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy">
458 <svg class="octicon octicon-star v-align-text-bottom" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74L14 6z"/></svg>
459 Star
460 </a>
461 <a class="social-count js-social-count" href="/johnheap/VAPPER-Galaxy/stargazers"
462 aria-label="0 users starred this repository">
463 0
464 </a>
465
466 </li>
467
468 <li>
469 <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to fork a repository" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;repo details fork button&quot;,&quot;repository_id&quot;:139730674,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A691:31FC:5350A:9C70E:5CF5626C&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="f1fd12af9e16afa9f9169bba4e92280efdd13b9f988453b683991c292a94ee58" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy">
470 <svg class="octicon octicon-repo-forked v-align-text-bottom" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
471 Fork
472 </a>
473 <a href="/johnheap/VAPPER-Galaxy/network/members" class="social-count"
474 aria-label="0 users forked this repository">
475 0
476 </a>
477 </li>
478 </ul>
479
480 <h1 class="public ">
481 <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><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>
482 <span class="author" itemprop="author"><a class="url fn" rel="author" data-hovercard-type="user" data-hovercard-url="/hovercards?user_id=24318980" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/johnheap">johnheap</a></span><!--
483 --><span class="path-divider">/</span><!--
484 --><strong itemprop="name"><a data-pjax="#js-repo-pjax-container" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a></strong>
485
486
487 </h1>
488
489 </div>
490
491 <nav class="hx_reponav reponav js-repo-nav js-sidenav-container-pjax container-lg p-responsive d-none d-lg-block"
492 itemscope
493 itemtype="http://schema.org/BreadcrumbList"
494 aria-label="Repository"
495 data-pjax="#js-repo-pjax-container">
496
497 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
498 <a class="js-selected-navigation-item selected reponav-item" itemprop="url" data-hotkey="g c" aria-current="page" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /johnheap/VAPPER-Galaxy" href="/johnheap/VAPPER-Galaxy">
499 <svg class="octicon octicon-code" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M9.5 3L8 4.5 11.5 8 8 11.5 9.5 13 14 8 9.5 3zm-5 0L0 8l4.5 5L6 11.5 2.5 8 6 4.5 4.5 3z"/></svg>
500 <span itemprop="name">Code</span>
501 <meta itemprop="position" content="1">
502 </a> </span>
503
504 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
505 <a itemprop="url" data-hotkey="g i" class="js-selected-navigation-item reponav-item" data-selected-links="repo_issues repo_labels repo_milestones /johnheap/VAPPER-Galaxy/issues" href="/johnheap/VAPPER-Galaxy/issues">
506 <svg class="octicon octicon-issue-opened" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"/></svg>
507 <span itemprop="name">Issues</span>
508 <span class="Counter">0</span>
509 <meta itemprop="position" content="2">
510 </a> </span>
511
512 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
513 <a data-hotkey="g p" itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /johnheap/VAPPER-Galaxy/pulls" href="/johnheap/VAPPER-Galaxy/pulls">
514 <svg class="octicon octicon-git-pull-request" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
515 <span itemprop="name">Pull requests</span>
516 <span class="Counter">0</span>
517 <meta itemprop="position" content="3">
518 </a> </span>
519
520
521 <a data-hotkey="g b" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /johnheap/VAPPER-Galaxy/projects" href="/johnheap/VAPPER-Galaxy/projects">
522 <svg class="octicon octicon-project" viewBox="0 0 15 16" version="1.1" width="15" height="16" aria-hidden="true"><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>
523 Projects
524 <span class="Counter" >0</span>
525 </a>
526
527
528 <a data-skip-pjax="true" class="js-selected-navigation-item reponav-item" data-selected-links="security alerts policy /johnheap/VAPPER-Galaxy/security/advisories" href="/johnheap/VAPPER-Galaxy/security/advisories">
529 <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" class="octicon" height="16px" width="16px">
530 <path fill-rule="evenodd" clip-rule="evenodd" d="M1 2l7-2 7 2v6.02C15 12.69 9.69 16 8 16c-1.69 0-7-3.31-7-7.98V2zm1 .75L8 1l6 1.75v5.268C14 12.104 9.45 15 8 15c-1.45 0-6-2.896-6-6.982V2.75z"></path>
531 <path d="M3 3.5L8 2v12c-1.207 0-5-2.482-5-5.985V3.5z"></path>
532 </svg>
533
534 Security
535 </a>
536 <a class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors dependency_graph pulse people /johnheap/VAPPER-Galaxy/pulse" href="/johnheap/VAPPER-Galaxy/pulse">
537 <svg class="octicon octicon-graph" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg>
538 Insights
539 </a>
540
541 </nav>
542
543 <div class="reponav-wrapper reponav-small d-lg-none">
544 <nav class="reponav js-reponav text-center no-wrap"
545 itemscope
546 itemtype="http://schema.org/BreadcrumbList">
547
548 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
549 <a class="js-selected-navigation-item selected reponav-item" itemprop="url" aria-current="page" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /johnheap/VAPPER-Galaxy" href="/johnheap/VAPPER-Galaxy">
550 <span itemprop="name">Code</span>
551 <meta itemprop="position" content="1">
552 </a> </span>
553
554 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
555 <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_issues repo_labels repo_milestones /johnheap/VAPPER-Galaxy/issues" href="/johnheap/VAPPER-Galaxy/issues">
556 <span itemprop="name">Issues</span>
557 <span class="Counter">0</span>
558 <meta itemprop="position" content="2">
559 </a> </span>
560
561 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
562 <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /johnheap/VAPPER-Galaxy/pulls" href="/johnheap/VAPPER-Galaxy/pulls">
563 <span itemprop="name">Pull requests</span>
564 <span class="Counter">0</span>
565 <meta itemprop="position" content="3">
566 </a> </span>
567
568 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
569 <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /johnheap/VAPPER-Galaxy/projects" href="/johnheap/VAPPER-Galaxy/projects">
570 <span itemprop="name">Projects</span>
571 <span class="Counter">0</span>
572 <meta itemprop="position" content="4">
573 </a> </span>
574
575
576 <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="security alerts policy /johnheap/VAPPER-Galaxy/security/advisories" href="/johnheap/VAPPER-Galaxy/security/advisories">
577 <span itemprop="name">Security</span>
578 <meta itemprop="position" content="6">
579 </a>
580 <a class="js-selected-navigation-item reponav-item" data-selected-links="pulse /johnheap/VAPPER-Galaxy/pulse" href="/johnheap/VAPPER-Galaxy/pulse">
581 Pulse
582 </a>
583
584 </nav>
585 </div>
586
587
588 </div>
589 <div class="container-lg new-discussion-timeline experiment-repo-nav p-responsive">
590 <div class="repository-content ">
591
592
593
594
595
596
597
598 <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/johnheap/VAPPER-Galaxy/blob/a4e16d71fe985f389930c02f94354b87d3aabadb/Tryp_V_T.py">Permalink</a>
599
600 <!-- blob contrib key: blob_contributors:v21:9b80d5431ee2c66dc8d0bd669b319131 -->
601 <div class="signup-prompt-bg rounded-1">
602 <div class="signup-prompt p-4 text-center mb-4 rounded-1">
603 <div class="position-relative">
604 <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/prompt_dismissals/signup" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="&#x2713;" /><input type="hidden" name="_method" value="put" /><input type="hidden" name="authenticity_token" value="u8vaE+nJK1t8+Agdc/ZN/ZDEQ1zDW1rahinuGQ03qeICRZPwq5nUk+WWU12I6oJkTK1SE+lme9JaR2kcuAfQbQ==" />
605 <button type="submit" class="position-absolute top-0 right-0 btn-link link-gray" data-ga-click="(Logged out) Sign up prompt, clicked Dismiss, text:dismiss">
606 Dismiss
607 </button>
608 </form> <h3 class="pt-2">Join GitHub today</h3>
609 <p class="col-6 mx-auto">GitHub is home to over 36 million developers working together to host and review code, manage projects, and build software together.</p>
610 <a class="btn btn-primary" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;files signup prompt&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A691:31FC:5350A:9C70E:5CF5626C&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="4bf7c9cc5dabe6e4cbd6bb6269757b356cdffe6bf9214fa28ed8854e1073068e" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up" href="/join?source=prompt-blob-show">Sign up</a>
611 </div>
612 </div>
613 </div>
614
615
616 <div class="d-flex flex-items-start flex-shrink-0 mb-2 flex-column flex-md-row">
617 <span class="d-flex flex-justify-between width-full width-md-auto">
618
619 <details class="details-reset details-overlay select-menu branch-select-menu hx_rsm" id="branch-select-menu">
620 <summary class="btn btn-sm select-menu-button css-truncate"
621 data-hotkey="w"
622
623 title="Switch branches or tags">
624 <i>Branch:</i>
625 <span class="css-truncate-target">master</span>
626 </summary>
627
628 <details-menu class="select-menu-modal hx_rsm-modal position-absolute" style="z-index: 99;" src="/johnheap/VAPPER-Galaxy/ref-list/master/Tryp_V_T.py?source_action=show&amp;source_controller=blob" preload>
629 <include-fragment class="select-menu-loading-overlay anim-pulse">
630 <svg height="32" class="octicon octicon-octoface" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M14.7 5.34c.13-.32.55-1.59-.13-3.31 0 0-1.05-.33-3.44 1.3-1-.28-2.07-.32-3.13-.32s-2.13.04-3.13.32c-2.39-1.64-3.44-1.3-3.44-1.3-.68 1.72-.26 2.99-.13 3.31C.49 6.21 0 7.33 0 8.69 0 13.84 3.33 15 7.98 15S16 13.84 16 8.69c0-1.36-.49-2.48-1.3-3.35zM8 14.02c-3.3 0-5.98-.15-5.98-3.35 0-.76.38-1.48 1.02-2.07 1.07-.98 2.9-.46 4.96-.46 2.07 0 3.88-.52 4.96.46.65.59 1.02 1.3 1.02 2.07 0 3.19-2.68 3.35-5.98 3.35zM5.49 9.01c-.66 0-1.2.8-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.54-1.78-1.2-1.78zm5.02 0c-.66 0-1.2.79-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.53-1.78-1.2-1.78z"/></svg>
631 </include-fragment>
632 </details-menu>
633 </details>
634
635 <div class="BtnGroup flex-shrink-0 d-md-none">
636 <a href="/johnheap/VAPPER-Galaxy/find/master"
637 class="js-pjax-capture-input btn btn-sm BtnGroup-item"
638 data-pjax
639 data-hotkey="t">
640 Find file
641 </a>
642 <clipboard-copy value="Tryp_V_T.py" class="btn btn-sm BtnGroup-item">
643 Copy path
644 </clipboard-copy>
645 </div>
646 </span>
647 <h2 id="blob-path" class="breadcrumb flex-auto min-width-0 text-normal flex-md-self-center ml-md-2 mr-md-3 my-2 my-md-0">
648 <span class="js-repo-root text-bold"><span class="js-path-segment"><a data-pjax="true" href="/johnheap/VAPPER-Galaxy"><span>VAPPER-Galaxy</span></a></span></span><span class="separator">/</span><strong class="final-path">Tryp_V_T.py</strong>
649 </h2>
650
651 <div class="BtnGroup flex-shrink-0 d-none d-md-inline-block">
652 <a href="/johnheap/VAPPER-Galaxy/find/master"
653 class="js-pjax-capture-input btn btn-sm BtnGroup-item"
654 data-pjax
655 data-hotkey="t">
656 Find file
657 </a>
658 <clipboard-copy value="Tryp_V_T.py" class="btn btn-sm BtnGroup-item">
659 Copy path
660 </clipboard-copy>
661 </div>
662 </div>
663
664
665
666 <include-fragment src="/johnheap/VAPPER-Galaxy/contributors/master/Tryp_V_T.py" class="Box Box--condensed commit-loader">
667 <div class="Box-body bg-blue-light f6">
668 Fetching contributors&hellip;
669 </div>
670
671 <div class="Box-body d-flex flex-items-center" >
672 <img alt="" class="loader-loading mr-2" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" />
673 <span class="text-red h6 loader-error">Cannot retrieve contributors at this time</span>
674 </div>
675 </include-fragment>
676
677
678
679
680
681 <div class="Box mt-3 position-relative">
682
683 <div class="Box-header py-2 d-flex flex-column flex-shrink-0 flex-md-row flex-md-items-center">
684
685 <div class="text-mono f6 flex-auto pr-3 flex-order-2 flex-md-order-1 mt-2 mt-md-0">
686 426 lines (349 sloc)
687 <span class="file-info-divider"></span>
688 17.3 KB
689 </div>
690
691 <div class="d-flex py-1 py-md-0 flex-auto flex-order-1 flex-md-order-2 flex-sm-grow-0 flex-justify-between">
692
693 <div class="BtnGroup">
694 <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/raw/master/Tryp_V_T.py">Raw</a>
695 <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/johnheap/VAPPER-Galaxy/blame/master/Tryp_V_T.py">Blame</a>
696 <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/Tryp_V_T.py">History</a>
697 </div>
698
699
700 <div>
701
702 <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw"
703 aria-label="You must be signed in to make or propose changes">
704 <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg>
705 </button>
706 <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw"
707 aria-label="You must be signed in to make or propose changes">
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">&quot;&quot;&quot;</span></span></td>
722 </tr>
723 <tr>
724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s">* Galaxy Version</span></td>
726 </tr>
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"></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"> * Copyright 2019 University of Liverpool</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"> * Author John Heap, Computational Biology Facility, UoL</span></td>
738 </tr>
739 <tr>
740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
741 <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Silva Pereira, Institute of Infection and Global Health, UoL</span></td>
742 </tr>
743 <tr>
744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
745 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
746 </tr>
747 <tr>
748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
749 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span></td>
750 </tr>
751 <tr>
752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
753 <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td>
754 </tr>
755 <tr>
756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
757 <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td>
758 </tr>
759 <tr>
760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
762 </tr>
763 <tr>
764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
765 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td>
766 </tr>
767 <tr>
768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
769 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
770 </tr>
771 <tr>
772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
773 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td>
774 </tr>
775 <tr>
776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
777 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span></td>
778 </tr>
779 <tr>
780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td>
782 </tr>
783 <tr>
784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td>
786 </tr>
787 <tr>
788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td>
790 </tr>
791 <tr>
792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
793 <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
794 </tr>
795 <tr>
796 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
797 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">&quot;&quot;&quot;</span></span></td>
798 </tr>
799 <tr>
800 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
801 <td id="LC21" class="blob-code blob-code-inner js-file-line">
802 </td>
803 </tr>
804 <tr>
805 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
806 <td id="LC22" class="blob-code blob-code-inner js-file-line">
807 </td>
808 </tr>
809 <tr>
810 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
811 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td>
812 </tr>
813 <tr>
814 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
815 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td>
816 </tr>
817 <tr>
818 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
819 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td>
820 </tr>
821 <tr>
822 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
823 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td>
824 </tr>
825 <tr>
826 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
827 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
828 </tr>
829 <tr>
830 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
831 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td>
832 </tr>
833 <tr>
834 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
835 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> import matplotlib as mpl</span></td>
836 </tr>
837 <tr>
838 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
839 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> mpl.use(&#39;Agg&#39;)</span></td>
840 </tr>
841 <tr>
842 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
843 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td>
844 </tr>
845 <tr>
846 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
847 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> numpy <span class="pl-k">as</span> np</td>
848 </tr>
849 <tr>
850 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
851 <td id="LC33" class="blob-code blob-code-inner js-file-line">
852 </td>
853 </tr>
854 <tr>
855 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
856 <td id="LC34" class="blob-code blob-code-inner js-file-line">
857 </td>
858 </tr>
859 <tr>
860 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
861 <td id="LC35" class="blob-code blob-code-inner js-file-line">
862 </td>
863 </tr>
864 <tr>
865 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
866 <td id="LC36" class="blob-code blob-code-inner js-file-line">
867 </td>
868 </tr>
869 <tr>
870 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
871 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> copies the user provided Fasta file to data/reference/file/file.fasta</span></td>
872 </tr>
873 <tr>
874 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
875 <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">uploadUserReferenceFastq</span>(<span class="pl-smi">refFastq</span>):</td>
876 </tr>
877 <tr>
878 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
879 <td id="LC39" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td>
880 </tr>
881 <tr>
882 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
883 <td id="LC40" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> &#39;mydata/test.fasta&#39; -&gt; &#39;test&#39;</span></td>
884 </tr>
885 <tr>
886 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
887 <td id="LC41" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td>
888 </tr>
889 <tr>
890 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
891 <td id="LC42" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> ref <span class="pl-c"><span class="pl-c">#</span>propose putting file in &#39;/data/reference/ref/</span></td>
892 </tr>
893 <tr>
894 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
895 <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-k">not</span> os.path.isdir(refDir): <span class="pl-c"><span class="pl-c">#</span> if directory data/Reference/ref doesn&#39;t exist</span></td>
896 </tr>
897 <tr>
898 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
899 <td id="LC44" class="blob-code blob-code-inner js-file-line"> os.mkdir(refDir)</td>
900 </tr>
901 <tr>
902 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
903 <td id="LC45" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> refDir<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span></td>
904 </tr>
905 <tr>
906 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
907 <td id="LC46" class="blob-code blob-code-inner js-file-line"> shutil.copy(refFastq, refPath <span class="pl-k">+</span> refBase) <span class="pl-c"><span class="pl-c">#</span>copy reference file into the directory</span></td>
908 </tr>
909 <tr>
910 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
911 <td id="LC47" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2-build <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> refPath <span class="pl-k">+</span> refBase<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>refPath<span class="pl-k">+</span>ref</td>
912 </tr>
913 <tr>
914 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
915 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>Building the bowtie2 reference files.<span class="pl-pds">&quot;</span></span>)</td>
916 </tr>
917 <tr>
918 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
919 <td id="LC49" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
920 </tr>
921 <tr>
922 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
923 <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td>
924 </tr>
925 <tr>
926 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
927 <td id="LC51" class="blob-code blob-code-inner js-file-line">
928 </td>
929 </tr>
930 <tr>
931 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
932 <td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptMapping</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">refFastq</span>, <span class="pl-smi">forwardFN</span>, <span class="pl-smi">reverseFN</span>):</td>
933 </tr>
934 <tr>
935 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
936 <td id="LC53" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> where is our Reference data?</span></td>
937 </tr>
938 <tr>
939 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
940 <td id="LC54" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td>
941 </tr>
942 <tr>
943 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
944 <td id="LC55" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>]</td>
945 </tr>
946 <tr>
947 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
948 <td id="LC56" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
949 </tr>
950 <tr>
951 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
952 <td id="LC57" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span></td>
953 </tr>
954 <tr>
955 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
956 <td id="LC58" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> refDir <span class="pl-k">+</span> ref</td>
957 </tr>
958 <tr>
959 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
960 <td id="LC59" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> now have reference file so we can proceed with the transcript mapping via bowtie2</span></td>
961 </tr>
962 <tr>
963 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
964 <td id="LC60" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2 -x <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -1 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>forwardFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -2 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>reverseFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -S <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sam<span class="pl-pds">&quot;</span></span></td>
965 </tr>
966 <tr>
967 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
968 <td id="LC61" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
969 </tr>
970 <tr>
971 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
972 <td id="LC62" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>) <span class="pl-c"><span class="pl-c">#</span>outputs a name.sam file</span></td>
973 </tr>
974 <tr>
975 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
976 <td id="LC63" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td>
977 </tr>
978 <tr>
979 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
980 <td id="LC64" class="blob-code blob-code-inner js-file-line">
981 </td>
982 </tr>
983 <tr>
984 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
985 <td id="LC65" class="blob-code blob-code-inner js-file-line">
986 </td>
987 </tr>
988 <tr>
989 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
990 <td id="LC66" class="blob-code blob-code-inner js-file-line">
991 </td>
992 </tr>
993 <tr>
994 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
995 <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">processSamFiles</span>(<span class="pl-smi">inputname</span>):</td>
996 </tr>
997 <tr>
998 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
999 <td id="LC68" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td>
1000 </tr>
1001 <tr>
1002 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
1003 <td id="LC69" class="blob-code blob-code-inner js-file-line"> samName <span class="pl-k">=</span> cur_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname</td>
1004 </tr>
1005 <tr>
1006 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
1007 <td id="LC70" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools view -bS <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sam &gt; <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.bam<span class="pl-pds">&quot;</span></span></td>
1008 </tr>
1009 <tr>
1010 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
1011 <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
1012 </tr>
1013 <tr>
1014 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
1015 <td id="LC72" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1016 </tr>
1017 <tr>
1018 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
1019 <td id="LC73" class="blob-code blob-code-inner js-file-line">
1020 </td>
1021 </tr>
1022 <tr>
1023 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
1024 <td id="LC74" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools sort <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.bam -o <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted<span class="pl-pds">&quot;</span></span></td>
1025 </tr>
1026 <tr>
1027 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
1028 <td id="LC75" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>argstring = <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>argString)</td>
1029 </tr>
1030 <tr>
1031 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
1032 <td id="LC76" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1033 </tr>
1034 <tr>
1035 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
1036 <td id="LC77" class="blob-code blob-code-inner js-file-line">
1037 </td>
1038 </tr>
1039 <tr>
1040 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
1041 <td id="LC78" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools index <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted.bai<span class="pl-pds">&quot;</span></span></td>
1042 </tr>
1043 <tr>
1044 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
1045 <td id="LC79" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>argstring = <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> argString)</td>
1046 </tr>
1047 <tr>
1048 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
1049 <td id="LC80" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1050 </tr>
1051 <tr>
1052 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
1053 <td id="LC81" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c"><span class="pl-c">#</span>we have saved out the relevent name.bam, name.sorted and name.sorted.bai files</span></td>
1054 </tr>
1055 <tr>
1056 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
1057 <td id="LC82" class="blob-code blob-code-inner js-file-line">
1058 </td>
1059 </tr>
1060 <tr>
1061 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
1062 <td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> we will not have the .gtf file so call cufflinks without -G option</span></td>
1063 </tr>
1064 <tr>
1065 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
1066 <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptAbundance</span>(<span class="pl-smi">inputname</span>):</td>
1067 </tr>
1068 <tr>
1069 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
1070 <td id="LC85" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>cufflinks -o <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.cuff -u -p 8 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted<span class="pl-pds">&quot;</span></span></td>
1071 </tr>
1072 <tr>
1073 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
1074 <td id="LC86" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td>
1075 </tr>
1076 <tr>
1077 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
1078 <td id="LC87" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted<span class="pl-pds">&quot;</span></span>) <span class="pl-c"><span class="pl-c">#</span>remove name.sorted</span></td>
1079 </tr>
1080 <tr>
1081 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
1082 <td id="LC88" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted.bai<span class="pl-pds">&quot;</span></span>)</td>
1083 </tr>
1084 <tr>
1085 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
1086 <td id="LC89" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.bam<span class="pl-pds">&quot;</span></span>)</td>
1087 </tr>
1088 <tr>
1089 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
1090 <td id="LC90" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td>
1091 </tr>
1092 <tr>
1093 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
1094 <td id="LC91" class="blob-code blob-code-inner js-file-line">
1095 </td>
1096 </tr>
1097 <tr>
1098 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
1099 <td id="LC92" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptsForBlast</span>(<span class="pl-smi">name</span>, <span class="pl-smi">refFastq</span>):</td>
1100 </tr>
1101 <tr>
1102 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
1103 <td id="LC93" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> quick and dirty just to see.</span></td>
1104 </tr>
1105 <tr>
1106 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
1107 <td id="LC94" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td>
1108 </tr>
1109 <tr>
1110 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
1111 <td id="LC95" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> &#39;mydata/test.fasta&#39; -&gt; &#39;test&#39;</span></td>
1112 </tr>
1113 <tr>
1114 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
1115 <td id="LC96" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td>
1116 </tr>
1117 <tr>
1118 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
1119 <td id="LC97" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> refBase <span class="pl-c"><span class="pl-c">#</span> eg refPath = data/Reference/Trinity/Trinity.fasta</span></td>
1120 </tr>
1121 <tr>
1122 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
1123 <td id="LC98" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> used for dirty # refPath = &#39;Trinity.fasta&#39; # dirty one</span></td>
1124 </tr>
1125 <tr>
1126 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
1127 <td id="LC99" class="blob-code blob-code-inner js-file-line"> track_df <span class="pl-k">=</span> pd.read_csv(name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&#39;</span>.cuff/genes.fpkm_tracking<span class="pl-pds">&#39;</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span><span class="pl-cce">\t</span><span class="pl-pds">&#39;</span></span>)</td>
1128 </tr>
1129 <tr>
1130 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
1131 <td id="LC100" class="blob-code blob-code-inner js-file-line"> names <span class="pl-k">=</span> track_df[<span class="pl-s"><span class="pl-pds">&#39;</span>locus<span class="pl-pds">&#39;</span></span>]</td>
1132 </tr>
1133 <tr>
1134 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
1135 <td id="LC101" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(len(names))</span></td>
1136 </tr>
1137 <tr>
1138 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
1139 <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(names[:5])</span></td>
1140 </tr>
1141 <tr>
1142 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
1143 <td id="LC103" class="blob-code blob-code-inner js-file-line">
1144 </td>
1145 </tr>
1146 <tr>
1147 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
1148 <td id="LC104" class="blob-code blob-code-inner js-file-line"> nlist <span class="pl-k">=</span> []</td>
1149 </tr>
1150 <tr>
1151 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
1152 <td id="LC105" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(names)):</td>
1153 </tr>
1154 <tr>
1155 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
1156 <td id="LC106" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> names[n].find(<span class="pl-s"><span class="pl-pds">&#39;</span>:<span class="pl-pds">&#39;</span></span>)</td>
1157 </tr>
1158 <tr>
1159 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
1160 <td id="LC107" class="blob-code blob-code-inner js-file-line"> nlist.append(names[n][:i])</td>
1161 </tr>
1162 <tr>
1163 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
1164 <td id="LC108" class="blob-code blob-code-inner js-file-line"> nameset <span class="pl-k">=</span> <span class="pl-c1">set</span>(nlist) <span class="pl-c"><span class="pl-c">#</span>get unique.</span></td>
1165 </tr>
1166 <tr>
1167 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
1168 <td id="LC109" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(refPath, <span class="pl-s"><span class="pl-pds">&#39;</span>r<span class="pl-pds">&#39;</span></span>) <span class="pl-k">as</span> myRef:</td>
1169 </tr>
1170 <tr>
1171 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
1172 <td id="LC110" class="blob-code blob-code-inner js-file-line"> refData <span class="pl-k">=</span> myRef.read()</td>
1173 </tr>
1174 <tr>
1175 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
1176 <td id="LC111" class="blob-code blob-code-inner js-file-line"> refData<span class="pl-k">=</span> refData<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&#39;</span><span class="pl-cce">\n</span>&gt;<span class="pl-pds">&#39;</span></span></td>
1177 </tr>
1178 <tr>
1179 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
1180 <td id="LC112" class="blob-code blob-code-inner js-file-line">
1181 </td>
1182 </tr>
1183 <tr>
1184 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
1185 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&#39;</span>_for_blast.fa<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>w<span class="pl-pds">&#39;</span></span>) <span class="pl-k">as</span> outfile:</td>
1186 </tr>
1187 <tr>
1188 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
1189 <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> trans_id <span class="pl-k">in</span> nameset:</td>
1190 </tr>
1191 <tr>
1192 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
1193 <td id="LC115" class="blob-code blob-code-inner js-file-line"> namepos <span class="pl-k">=</span> refData.find(trans_id)</td>
1194 </tr>
1195 <tr>
1196 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
1197 <td id="LC116" class="blob-code blob-code-inner js-file-line"> endpos <span class="pl-k">=</span> refData.find(<span class="pl-s"><span class="pl-pds">&#39;</span>&gt;<span class="pl-pds">&#39;</span></span>, namepos)</td>
1198 </tr>
1199 <tr>
1200 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
1201 <td id="LC117" class="blob-code blob-code-inner js-file-line"> outfile.write(<span class="pl-s"><span class="pl-pds">&#39;</span>&gt;<span class="pl-pds">&#39;</span></span><span class="pl-k">+</span>refData[namepos:endpos])</td>
1202 </tr>
1203 <tr>
1204 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
1205 <td id="LC118" class="blob-code blob-code-inner js-file-line">
1206 </td>
1207 </tr>
1208 <tr>
1209 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
1210 <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td>
1211 </tr>
1212 <tr>
1213 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
1214 <td id="LC120" class="blob-code blob-code-inner js-file-line">
1215 </td>
1216 </tr>
1217 <tr>
1218 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
1219 <td id="LC121" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">html_resource</span>, <span class="pl-smi">database</span>):</td>
1220 </tr>
1221 <tr>
1222 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
1223 <td id="LC122" class="blob-code blob-code-inner js-file-line"> db_path <span class="pl-k">=</span> database</td>
1224 </tr>
1225 <tr>
1226 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
1227 <td id="LC123" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>blastx -db <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -query <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_for_blast.fa -outfmt 10 -out <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_blast.txt<span class="pl-pds">&quot;</span></span></td>
1228 </tr>
1229 <tr>
1230 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
1231 <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
1232 </tr>
1233 <tr>
1234 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
1235 <td id="LC125" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1236 </tr>
1237 <tr>
1238 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
1239 <td id="LC126" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
1240 </tr>
1241 <tr>
1242 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
1243 <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Error in blastall<span class="pl-pds">&quot;</span></span></td>
1244 </tr>
1245 <tr>
1246 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
1247 <td id="LC128" class="blob-code blob-code-inner js-file-line"> blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_blast.txt<span class="pl-pds">&quot;</span></span>)</td>
1248 </tr>
1249 <tr>
1250 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
1251 <td id="LC129" class="blob-code blob-code-inner js-file-line"> blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>length<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>mismatch<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>gapopen<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>qstart<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>qend<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>sstart<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>send<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>bitscore<span class="pl-pds">&#39;</span></span>]</td>
1252 </tr>
1253 <tr>
1254 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
1255 <td id="LC130" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>]<span class="pl-k">&gt;=</span><span class="pl-c1">70</span>) <span class="pl-k">&amp;</span> (blast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>length<span class="pl-pds">&#39;</span></span>] <span class="pl-k">&gt;</span> <span class="pl-c1">100</span>) <span class="pl-k">&amp;</span> (blast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>] <span class="pl-k">&lt;=</span><span class="pl-c1">0.001</span>) ]</td>
1256 </tr>
1257 <tr>
1258 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
1259 <td id="LC131" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>bitscore<span class="pl-pds">&#39;</span></span>]] <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td>
1260 </tr>
1261 <tr>
1262 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
1263 <td id="LC132" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> need to allocate the transcripts (if allocated more than once to the phylotype with least error.</span></td>
1264 </tr>
1265 <tr>
1266 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
1267 <td id="LC133" class="blob-code blob-code-inner js-file-line"> transcripts <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>]</td>
1268 </tr>
1269 <tr>
1270 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
1271 <td id="LC134" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>bitscore<span class="pl-pds">&#39;</span></span>])</td>
1272 </tr>
1273 <tr>
1274 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
1275 <td id="LC135" class="blob-code blob-code-inner js-file-line"> transSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(transcripts)</td>
1276 </tr>
1277 <tr>
1278 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
1279 <td id="LC136" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> t <span class="pl-k">in</span> transSet:</td>
1280 </tr>
1281 <tr>
1282 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
1283 <td id="LC137" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> blastResult_df[(blastResult_df[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> t)]</td>
1284 </tr>
1285 <tr>
1286 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
1287 <td id="LC138" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get one with smallest error value</span></td>
1288 </tr>
1289 <tr>
1290 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
1291 <td id="LC139" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(t + &quot;:&quot;)</span></td>
1292 </tr>
1293 <tr>
1294 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
1295 <td id="LC140" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(temp_df)</span></td>
1296 </tr>
1297 <tr>
1298 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
1299 <td id="LC141" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> temp_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>])</td>
1300 </tr>
1301 <tr>
1302 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
1303 <td id="LC142" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> b_df.append(temp_df.iloc[[<span class="pl-c1">0</span>]])</td>
1304 </tr>
1305 <tr>
1306 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
1307 <td id="LC143" class="blob-code blob-code-inner js-file-line">
1308 </td>
1309 </tr>
1310 <tr>
1311 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
1312 <td id="LC144" class="blob-code blob-code-inner js-file-line"> b_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>])</td>
1313 </tr>
1314 <tr>
1315 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
1316 <td id="LC145" class="blob-code blob-code-inner js-file-line"> b_df.to_csv(test_name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&#39;</span>_transcript.csv<span class="pl-pds">&#39;</span></span>)</td>
1317 </tr>
1318 <tr>
1319 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
1320 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> b_df</td>
1321 </tr>
1322 <tr>
1323 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
1324 <td id="LC147" class="blob-code blob-code-inner js-file-line">
1325 </td>
1326 </tr>
1327 <tr>
1328 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
1329 <td id="LC148" class="blob-code blob-code-inner js-file-line">
1330 </td>
1331 </tr>
1332 <tr>
1333 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
1334 <td id="LC149" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createMultiHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">composite_df</span>):</td>
1335 </tr>
1336 <tr>
1337 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
1338 <td id="LC150" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td>
1339 </tr>
1340 <tr>
1341 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
1342 <td id="LC151" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;html&gt;&lt;title&gt;T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span>&lt;/title&gt;&lt;body&gt;&lt;div style=&#39;text-align:center&#39;&gt;&lt;h2&gt;&lt;i&gt;Trypanosoma vivax&lt;/i&gt; Variant Antigen Profile&lt;/h2&gt;&lt;h3&gt;<span class="pl-pds">&quot;</span></span></td>
1343 </tr>
1344 <tr>
1345 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
1346 <td id="LC152" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>Sample name: <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]</td>
1347 </tr>
1348 <tr>
1349 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
1350 <td id="LC153" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;br&gt;Transcriptomic Analysis&lt;/h3&gt;&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
1351 </tr>
1352 <tr>
1353 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
1354 <td id="LC154" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;p style = &#39;margin-left:20%; margin-right:20%&#39;&gt;Legend: <span class="pl-pds">&quot;</span></span> \</td>
1355 </tr>
1356 <tr>
1357 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
1358 <td id="LC155" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Variant Antigen Profile of a &lt;i&gt;Trypanosoma vivax&lt;/i&gt; transcriptomes. <span class="pl-pds">&quot;</span></span> \</td>
1359 </tr>
1360 <tr>
1361 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
1362 <td id="LC156" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">&quot;</span></span> \</td>
1363 </tr>
1364 <tr>
1365 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
1366 <td id="LC157" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">&quot;</span></span> \</td>
1367 </tr>
1368 <tr>
1369 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
1370 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">&quot;</span></span> \</td>
1371 </tr>
1372 <tr>
1373 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
1374 <td id="LC159" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>(Silva Pereira et al., 2019).&lt;/p&gt; <span class="pl-pds">&quot;</span></span></td>
1375 </tr>
1376 <tr>
1377 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
1378 <td id="LC160" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;style&gt; table, th, tr, td {border: 1px solid black; border-collapse: collapse;}&lt;/style&gt;<span class="pl-pds">&quot;</span></span></td>
1379 </tr>
1380 <tr>
1381 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
1382 <td id="LC161" class="blob-code blob-code-inner js-file-line">
1383 </td>
1384 </tr>
1385 <tr>
1386 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
1387 <td id="LC162" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;table style=&#39;width:50%;margin-left:25%;text-align:center&#39;&gt;&lt;tr&gt;&lt;th&gt;Phylotype&lt;/th&gt;<span class="pl-pds">&quot;</span></span></td>
1388 </tr>
1389 <tr>
1390 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
1391 <td id="LC163" class="blob-code blob-code-inner js-file-line"> wLists <span class="pl-k">=</span> []</td>
1392 </tr>
1393 <tr>
1394 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
1395 <td id="LC164" class="blob-code blob-code-inner js-file-line">
1396 </td>
1397 </tr>
1398 <tr>
1399 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
1400 <td id="LC165" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>,<span class="pl-c1">len</span>(labelList)):</td>
1401 </tr>
1402 <tr>
1403 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
1404 <td id="LC166" class="blob-code blob-code-inner js-file-line"> wLists.append(composite_df[labelList[j]])</td>
1405 </tr>
1406 <tr>
1407 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
1408 <td id="LC167" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;th&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(labelList[j]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/th&gt;<span class="pl-pds">&quot;</span></span></td>
1409 </tr>
1410 <tr>
1411 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
1412 <td id="LC168" class="blob-code blob-code-inner js-file-line">
1413 </td>
1414 </tr>
1415 <tr>
1416 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
1417 <td id="LC169" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/tr&gt;<span class="pl-cce">\n</span><span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> header</td>
1418 </tr>
1419 <tr>
1420 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
1421 <td id="LC170" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span></td>
1422 </tr>
1423 <tr>
1424 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
1425 <td id="LC171" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> composite_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>]</td>
1426 </tr>
1427 <tr>
1428 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
1429 <td id="LC172" class="blob-code blob-code-inner js-file-line">
1430 </td>
1431 </tr>
1432 <tr>
1433 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
1434 <td id="LC173" class="blob-code blob-code-inner js-file-line">
1435 </td>
1436 </tr>
1437 <tr>
1438 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
1439 <td id="LC174" class="blob-code blob-code-inner js-file-line">
1440 </td>
1441 </tr>
1442 <tr>
1443 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
1444 <td id="LC175" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(composite_df)):</td>
1445 </tr>
1446 <tr>
1447 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
1448 <td id="LC176" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;tr&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phyList[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;<span class="pl-pds">&quot;</span></span></td>
1449 </tr>
1450 <tr>
1451 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
1452 <td id="LC177" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span>):</td>
1453 </tr>
1454 <tr>
1455 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
1456 <td id="LC178" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(j)</span></td>
1457 </tr>
1458 <tr>
1459 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
1460 <td id="LC179" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(wLists[j][i], <span class="pl-s"><span class="pl-pds">&#39;</span>.4f<span class="pl-pds">&#39;</span></span>)</td>
1461 </tr>
1462 <tr>
1463 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
1464 <td id="LC180" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;<span class="pl-pds">&quot;</span></span></td>
1465 </tr>
1466 <tr>
1467 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
1468 <td id="LC181" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/tr&gt;<span class="pl-cce">\n</span><span class="pl-pds">&quot;</span></span></td>
1469 </tr>
1470 <tr>
1471 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
1472 <td id="LC182" class="blob-code blob-code-inner js-file-line">
1473 </td>
1474 </tr>
1475 <tr>
1476 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
1477 <td id="LC183" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/table&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
1478 </tr>
1479 <tr>
1480 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
1481 <td id="LC184" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;h3&gt;Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span>&lt;/h3&gt;<span class="pl-pds">&quot;</span></span></td>
1482 </tr>
1483 <tr>
1484 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
1485 <td id="LC185" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;img src = &#39;<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_phylotypes.png&#39; alt=&#39;Bar chart of phylotype variation&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
1486 </tr>
1487 <tr>
1488 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
1489 <td id="LC186" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
1490 </tr>
1491 <tr>
1492 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
1493 <td id="LC187" class="blob-code blob-code-inner js-file-line">
1494 </td>
1495 </tr>
1496 <tr>
1497 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
1498 <td id="LC188" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>], <span class="pl-s"><span class="pl-pds">&quot;</span>w<span class="pl-pds">&quot;</span></span>) <span class="pl-k">as</span> htmlfile:</td>
1499 </tr>
1500 <tr>
1501 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
1502 <td id="LC189" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
1503 </tr>
1504 <tr>
1505 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
1506 <td id="LC190" class="blob-code blob-code-inner js-file-line">
1507 </td>
1508 </tr>
1509 <tr>
1510 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
1511 <td id="LC191" class="blob-code blob-code-inner js-file-line">
1512 </td>
1513 </tr>
1514 <tr>
1515 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
1516 <td id="LC192" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">sum_df</span>):</td>
1517 </tr>
1518 <tr>
1519 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
1520 <td id="LC193" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
1521 </tr>
1522 <tr>
1523 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
1524 <td id="LC194" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;html&gt;&lt;title&gt;T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span>&lt;/title&gt;&lt;body&gt;&lt;div style=&#39;text-align:center&#39;&gt;&lt;h2&gt;&lt;i&gt;Trypanosoma vivax&lt;/i&gt; Variant Antigen Profile&lt;/h2&gt;&lt;h3&gt;<span class="pl-pds">&quot;</span></span></td>
1525 </tr>
1526 <tr>
1527 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
1528 <td id="LC195" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>Sample name: <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]</td>
1529 </tr>
1530 <tr>
1531 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
1532 <td id="LC196" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;br&gt;Transcriptomic Analysis&lt;/h3&gt;&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
1533 </tr>
1534 <tr>
1535 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
1536 <td id="LC197" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;p style = &#39;margin-left:20%; margin-right:20%&#39;&gt;Legend: <span class="pl-pds">&quot;</span></span> \</td>
1537 </tr>
1538 <tr>
1539 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
1540 <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Variant Antigen Profile of a &lt;i&gt;Trypanosoma vivax&lt;/i&gt; transcriptome. <span class="pl-pds">&quot;</span></span> \</td>
1541 </tr>
1542 <tr>
1543 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
1544 <td id="LC199" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">&quot;</span></span> \</td>
1545 </tr>
1546 <tr>
1547 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
1548 <td id="LC200" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">&quot;</span></span> \</td>
1549 </tr>
1550 <tr>
1551 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
1552 <td id="LC201" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">&quot;</span></span> \</td>
1553 </tr>
1554 <tr>
1555 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
1556 <td id="LC202" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>(Silva Pereira et al., 2019).&lt;/p&gt; <span class="pl-pds">&quot;</span></span></td>
1557 </tr>
1558 <tr>
1559 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
1560 <td id="LC203" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;style&gt; table, th, tr, td {border: 1px solid black; border-collapse: collapse;}&lt;/style&gt;<span class="pl-pds">&quot;</span></span></td>
1561 </tr>
1562 <tr>
1563 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
1564 <td id="LC204" class="blob-code blob-code-inner js-file-line">
1565 </td>
1566 </tr>
1567 <tr>
1568 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
1569 <td id="LC205" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;table style=&#39;width:50%;table-layout: auto; margin-left:25%;text-align:center&#39;&gt;&lt;tr&gt;&lt;th&gt;Phylotype&lt;/th&gt;<span class="pl-pds">&quot;</span></span> \</td>
1570 </tr>
1571 <tr>
1572 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
1573 <td id="LC206" class="blob-code blob-code-inner js-file-line"> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;th&gt;Combined FPKM&lt;/th&gt;&lt;th&gt;Weighted Frequency&lt;/th&gt;&lt;/tr&gt;<span class="pl-pds">&quot;</span></span></td>
1574 </tr>
1575 <tr>
1576 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
1577 <td id="LC207" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span></td>
1578 </tr>
1579 <tr>
1580 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
1581 <td id="LC208" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></td>
1582 </tr>
1583 <tr>
1584 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
1585 <td id="LC209" class="blob-code blob-code-inner js-file-line"> phySeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>]</td>
1586 </tr>
1587 <tr>
1588 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
1589 <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> sacSeries = sum_df[&#39;saccver&#39;]</span></td>
1590 </tr>
1591 <tr>
1592 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
1593 <td id="LC211" class="blob-code blob-code-inner js-file-line"> fSeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>]</td>
1594 </tr>
1595 <tr>
1596 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
1597 <td id="LC212" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> fSeries.sum()</td>
1598 </tr>
1599 <tr>
1600 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
1601 <td id="LC213" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(&quot;Total=&quot;+str(total))</span></td>
1602 </tr>
1603 <tr>
1604 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
1605 <td id="LC214" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum_df)):</td>
1606 </tr>
1607 <tr>
1608 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
1609 <td id="LC215" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(phySeries[i])</span></td>
1610 </tr>
1611 <tr>
1612 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
1613 <td id="LC216" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i], <span class="pl-s"><span class="pl-pds">&#39;</span>.2f<span class="pl-pds">&#39;</span></span>)</td>
1614 </tr>
1615 <tr>
1616 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
1617 <td id="LC217" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i]<span class="pl-k">/</span>total, <span class="pl-s"><span class="pl-pds">&#39;</span>.2f<span class="pl-pds">&#39;</span></span>)</td>
1618 </tr>
1619 <tr>
1620 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
1621 <td id="LC218" class="blob-code blob-code-inner js-file-line">
1622 </td>
1623 </tr>
1624 <tr>
1625 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
1626 <td id="LC219" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>w = format(weightList[i], &#39;.4f&#39;)</span></td>
1627 </tr>
1628 <tr>
1629 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
1630 <td id="LC220" class="blob-code blob-code-inner js-file-line">
1631 </td>
1632 </tr>
1633 <tr>
1634 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
1635 <td id="LC221" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;tr&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phySeries[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(w)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/tr&gt;<span class="pl-pds">&quot;</span></span></td>
1636 </tr>
1637 <tr>
1638 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
1639 <td id="LC222" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/table&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
1640 </tr>
1641 <tr>
1642 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
1643 <td id="LC223" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;h3&gt;Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span>&lt;/h3&gt;<span class="pl-pds">&quot;</span></span></td>
1644 </tr>
1645 <tr>
1646 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
1647 <td id="LC224" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;img src = &#39;<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_phylotypes.png&#39; alt=&#39;Bar chart of phylotype variation&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
1648 </tr>
1649 <tr>
1650 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
1651 <td id="LC225" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
1652 </tr>
1653 <tr>
1654 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
1655 <td id="LC226" class="blob-code blob-code-inner js-file-line">
1656 </td>
1657 </tr>
1658 <tr>
1659 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
1660 <td id="LC227" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>], <span class="pl-s"><span class="pl-pds">&quot;</span>w<span class="pl-pds">&quot;</span></span>) <span class="pl-k">as</span> htmlfile:</td>
1661 </tr>
1662 <tr>
1663 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
1664 <td id="LC228" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
1665 </tr>
1666 <tr>
1667 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
1668 <td id="LC229" class="blob-code blob-code-inner js-file-line">
1669 </td>
1670 </tr>
1671 <tr>
1672 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
1673 <td id="LC230" class="blob-code blob-code-inner js-file-line">
1674 </td>
1675 </tr>
1676 <tr>
1677 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
1678 <td id="LC231" class="blob-code blob-code-inner js-file-line">
1679 </td>
1680 </tr>
1681 <tr>
1682 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
1683 <td id="LC232" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getPhyloNumber</span>(<span class="pl-smi">sac</span>):</td>
1684 </tr>
1685 <tr>
1686 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
1687 <td id="LC233" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> sac.find(<span class="pl-s"><span class="pl-pds">&#39;</span>_<span class="pl-pds">&#39;</span></span>)</td>
1688 </tr>
1689 <tr>
1690 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
1691 <td id="LC234" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c1">int</span>(sac[<span class="pl-c1">1</span>:i])</td>
1692 </tr>
1693 <tr>
1694 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
1695 <td id="LC235" class="blob-code blob-code-inner js-file-line">
1696 </td>
1697 </tr>
1698 <tr>
1699 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
1700 <td id="LC236" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">combineFPMK</span>(<span class="pl-smi">tdict</span>):</td>
1701 </tr>
1702 <tr>
1703 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
1704 <td id="LC237" class="blob-code blob-code-inner js-file-line"> fpkm_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&#39;</span>.cuff/genes.fpkm_tracking<span class="pl-pds">&#39;</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span><span class="pl-cce">\t</span><span class="pl-pds">&#39;</span></span>)</td>
1705 </tr>
1706 <tr>
1707 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
1708 <td id="LC238" class="blob-code blob-code-inner js-file-line">
1709 </td>
1710 </tr>
1711 <tr>
1712 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
1713 <td id="LC239" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fpkm_df = pd.read_csv(&#39;genes.fpkm_tracking&#39;,sep=&#39;\t&#39;)</span></td>
1714 </tr>
1715 <tr>
1716 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
1717 <td id="LC240" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td>
1718 </tr>
1719 <tr>
1720 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
1721 <td id="LC241" class="blob-code blob-code-inner js-file-line"> fpkm_df[<span class="pl-s"><span class="pl-pds">&#39;</span>locus<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> fpkm_df[<span class="pl-s"><span class="pl-pds">&#39;</span>locus<span class="pl-pds">&#39;</span></span>].apply(<span class="pl-k">lambda</span> <span class="pl-smi">names</span>: names[:names.find(<span class="pl-s"><span class="pl-pds">&#39;</span>:<span class="pl-pds">&#39;</span></span>)])</td>
1722 </tr>
1723 <tr>
1724 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
1725 <td id="LC242" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td>
1726 </tr>
1727 <tr>
1728 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
1729 <td id="LC243" class="blob-code blob-code-inner js-file-line"> reducedBlast_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&#39;</span>_transcript.csv<span class="pl-pds">&#39;</span></span>)</td>
1730 </tr>
1731 <tr>
1732 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
1733 <td id="LC244" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> reducedBlast_df = pd.read_csv(&#39;TrinityVT_transcript.csv&#39;)</span></td>
1734 </tr>
1735 <tr>
1736 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
1737 <td id="LC245" class="blob-code blob-code-inner js-file-line"> saccverSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(reducedBlast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>])</td>
1738 </tr>
1739 <tr>
1740 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
1741 <td id="LC246" class="blob-code blob-code-inner js-file-line"> saccverList <span class="pl-k">=</span> <span class="pl-c1">list</span>(saccverSet)</td>
1742 </tr>
1743 <tr>
1744 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
1745 <td id="LC247" class="blob-code blob-code-inner js-file-line"> saccverList.sort()</td>
1746 </tr>
1747 <tr>
1748 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
1749 <td id="LC248" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(saccverList[:5])</span></td>
1750 </tr>
1751 <tr>
1752 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
1753 <td id="LC249" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>])</td>
1754 </tr>
1755 <tr>
1756 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
1757 <td id="LC250" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> sv <span class="pl-k">in</span> saccverList:</td>
1758 </tr>
1759 <tr>
1760 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
1761 <td id="LC251" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(sv)</span></td>
1762 </tr>
1763 <tr>
1764 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
1765 <td id="LC252" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> reducedBlast_df[reducedBlast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> sv]</td>
1766 </tr>
1767 <tr>
1768 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
1769 <td id="LC253" class="blob-code blob-code-inner js-file-line"> qList <span class="pl-k">=</span> <span class="pl-c1">list</span>(temp_df[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>])</td>
1770 </tr>
1771 <tr>
1772 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
1773 <td id="LC254" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> q <span class="pl-k">in</span> qList:</td>
1774 </tr>
1775 <tr>
1776 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
1777 <td id="LC255" class="blob-code blob-code-inner js-file-line"> f_df <span class="pl-k">=</span> fpkm_df[(fpkm_df[<span class="pl-s"><span class="pl-pds">&#39;</span>locus<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> q)]</td>
1778 </tr>
1779 <tr>
1780 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
1781 <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-c1">len</span>(f_df) <span class="pl-k">&gt;</span> <span class="pl-c1">1</span>:</td>
1782 </tr>
1783 <tr>
1784 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
1785 <td id="LC257" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">&#39;</span>WARNING MULTIPLE FPKM<span class="pl-pds">&#39;</span></span>)</td>
1786 </tr>
1787 <tr>
1788 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
1789 <td id="LC258" class="blob-code blob-code-inner js-file-line"> new_fpkm<span class="pl-k">=</span><span class="pl-c1">list</span>(f_df[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>])</td>
1790 </tr>
1791 <tr>
1792 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
1793 <td id="LC259" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> (new_fpkm[<span class="pl-c1">0</span>])</td>
1794 </tr>
1795 <tr>
1796 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
1797 <td id="LC260" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(f)</span></td>
1798 </tr>
1799 <tr>
1800 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
1801 <td id="LC261" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> new_df.append({<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>: q, <span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>: sv, <span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>: f}, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1802 </tr>
1803 <tr>
1804 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
1805 <td id="LC262" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> new_df.groupby(<span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>)[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>].sum().reset_index()</td>
1806 </tr>
1807 <tr>
1808 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
1809 <td id="LC263" class="blob-code blob-code-inner js-file-line">
1810 </td>
1811 </tr>
1812 <tr>
1813 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
1814 <td id="LC264" class="blob-code blob-code-inner js-file-line"> FPKMsum_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> FPKMsum_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: getPhyloNumber(row[<span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>]), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
1815 </tr>
1816 <tr>
1817 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
1818 <td id="LC265" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>])</td>
1819 </tr>
1820 <tr>
1821 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
1822 <td id="LC266" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.reset_index(<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1823 </tr>
1824 <tr>
1825 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
1826 <td id="LC267" class="blob-code blob-code-inner js-file-line">
1827 </td>
1828 </tr>
1829 <tr>
1830 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
1831 <td id="LC268" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum_df)</span></td>
1832 </tr>
1833 <tr>
1834 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
1835 <td id="LC269" class="blob-code blob-code-inner js-file-line"> FPKMsum_df.to_csv(<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM_sum.csv<span class="pl-pds">&#39;</span></span>)</td>
1836 </tr>
1837 <tr>
1838 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
1839 <td id="LC270" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum_df.groupby(<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>)[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>].sum().reset_index()</td>
1840 </tr>
1841 <tr>
1842 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
1843 <td id="LC271" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum2_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>])</td>
1844 </tr>
1845 <tr>
1846 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
1847 <td id="LC272" class="blob-code blob-code-inner js-file-line">
1848 </td>
1849 </tr>
1850 <tr>
1851 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
1852 <td id="LC273" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum2_df)</span></td>
1853 </tr>
1854 <tr>
1855 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
1856 <td id="LC274" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df.to_csv(<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM_sum2.csv<span class="pl-pds">&#39;</span></span>) <span class="pl-c"><span class="pl-c">#</span> in case more than one entry for a particular phylotype</span></td>
1857 </tr>
1858 <tr>
1859 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
1860 <td id="LC275" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> FPKMsum_df, FPKMsum2_df</td>
1861 </tr>
1862 <tr>
1863 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
1864 <td id="LC276" class="blob-code blob-code-inner js-file-line">
1865 </td>
1866 </tr>
1867 <tr>
1868 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
1869 <td id="LC277" class="blob-code blob-code-inner js-file-line">
1870 </td>
1871 </tr>
1872 <tr>
1873 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
1874 <td id="LC278" class="blob-code blob-code-inner js-file-line">
1875 </td>
1876 </tr>
1877 <tr>
1878 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
1879 <td id="LC279" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">normalisef</span>(<span class="pl-smi">f</span>,<span class="pl-smi">max</span>):</td>
1880 </tr>
1881 <tr>
1882 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
1883 <td id="LC280" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> f<span class="pl-k">/</span><span class="pl-c1">max</span></td>
1884 </tr>
1885 <tr>
1886 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
1887 <td id="LC281" class="blob-code blob-code-inner js-file-line">
1888 </td>
1889 </tr>
1890 <tr>
1891 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
1892 <td id="LC282" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getComposite_sum2</span>(<span class="pl-smi">nameList</span>,<span class="pl-smi">sum2_dfs</span>):</td>
1893 </tr>
1894 <tr>
1895 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
1896 <td id="LC283" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> lets get a composite sum2_df from all of the sum2_dfs</span></td>
1897 </tr>
1898 <tr>
1899 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
1900 <td id="LC284" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> []</td>
1901 </tr>
1902 <tr>
1903 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
1904 <td id="LC285" class="blob-code blob-code-inner js-file-line">
1905 </td>
1906 </tr>
1907 <tr>
1908 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
1909 <td id="LC286" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td>
1910 </tr>
1911 <tr>
1912 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
1913 <td id="LC287" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>].sum()</td>
1914 </tr>
1915 <tr>
1916 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
1917 <td id="LC288" class="blob-code blob-code-inner js-file-line"> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">&#39;</span>w<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> sum2_dfs[i].apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>], total), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
1918 </tr>
1919 <tr>
1920 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
1921 <td id="LC289" class="blob-code blob-code-inner js-file-line"> pSeries <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>]</td>
1922 </tr>
1923 <tr>
1924 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
1925 <td id="LC290" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pSeries:</td>
1926 </tr>
1927 <tr>
1928 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
1929 <td id="LC291" class="blob-code blob-code-inner js-file-line"> phyList.append(p) <span class="pl-c"><span class="pl-c">#</span> get all the phylotypes in this one</span></td>
1930 </tr>
1931 <tr>
1932 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
1933 <td id="LC292" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> <span class="pl-c1">list</span>(<span class="pl-c1">set</span>(phyList))</td>
1934 </tr>
1935 <tr>
1936 <td id="L293" class="blob-num js-line-number" data-line-number="293"></td>
1937 <td id="LC293" class="blob-code blob-code-inner js-file-line"> phyList.sort()</td>
1938 </tr>
1939 <tr>
1940 <td id="L294" class="blob-num js-line-number" data-line-number="294"></td>
1941 <td id="LC294" class="blob-code blob-code-inner js-file-line"> composite_sum2_df <span class="pl-k">=</span> pd.DataFrame(phyList, <span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>])</td>
1942 </tr>
1943 <tr>
1944 <td id="L295" class="blob-num js-line-number" data-line-number="295"></td>
1945 <td id="LC295" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td>
1946 </tr>
1947 <tr>
1948 <td id="L296" class="blob-num js-line-number" data-line-number="296"></td>
1949 <td id="LC296" class="blob-code blob-code-inner js-file-line"> wList <span class="pl-k">=</span> []</td>
1950 </tr>
1951 <tr>
1952 <td id="L297" class="blob-num js-line-number" data-line-number="297"></td>
1953 <td id="LC297" class="blob-code blob-code-inner js-file-line"> pindf <span class="pl-k">=</span> <span class="pl-c1">list</span>(sum2_dfs[i][<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>])</td>
1954 </tr>
1955 <tr>
1956 <td id="L298" class="blob-num js-line-number" data-line-number="298"></td>
1957 <td id="LC298" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(pindf)</span></td>
1958 </tr>
1959 <tr>
1960 <td id="L299" class="blob-num js-line-number" data-line-number="299"></td>
1961 <td id="LC299" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> phyList:</td>
1962 </tr>
1963 <tr>
1964 <td id="L300" class="blob-num js-line-number" data-line-number="300"></td>
1965 <td id="LC300" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> p <span class="pl-k">in</span> pindf:</td>
1966 </tr>
1967 <tr>
1968 <td id="L301" class="blob-num js-line-number" data-line-number="301"></td>
1969 <td id="LC301" class="blob-code blob-code-inner js-file-line"> df <span class="pl-k">=</span> sum2_dfs[i]</td>
1970 </tr>
1971 <tr>
1972 <td id="L302" class="blob-num js-line-number" data-line-number="302"></td>
1973 <td id="LC302" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> df.loc[df[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> p, <span class="pl-s"><span class="pl-pds">&#39;</span>w<span class="pl-pds">&#39;</span></span>].iloc[<span class="pl-c1">0</span>]</td>
1974 </tr>
1975 <tr>
1976 <td id="L303" class="blob-num js-line-number" data-line-number="303"></td>
1977 <td id="LC303" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td>
1978 </tr>
1979 <tr>
1980 <td id="L304" class="blob-num js-line-number" data-line-number="304"></td>
1981 <td id="LC304" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
1982 </tr>
1983 <tr>
1984 <td id="L305" class="blob-num js-line-number" data-line-number="305"></td>
1985 <td id="LC305" class="blob-code blob-code-inner js-file-line"> wList.append(w)</td>
1986 </tr>
1987 <tr>
1988 <td id="L306" class="blob-num js-line-number" data-line-number="306"></td>
1989 <td id="LC306" class="blob-code blob-code-inner js-file-line"> composite_sum2_df[nameList[i]] <span class="pl-k">=</span> wList</td>
1990 </tr>
1991 <tr>
1992 <td id="L307" class="blob-num js-line-number" data-line-number="307"></td>
1993 <td id="LC307" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(composite_sum2_df)</span></td>
1994 </tr>
1995 <tr>
1996 <td id="L308" class="blob-num js-line-number" data-line-number="308"></td>
1997 <td id="LC308" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>composite_sum2_df.to_csv(&#39;composite.csv&#39;)</span></td>
1998 </tr>
1999 <tr>
2000 <td id="L309" class="blob-num js-line-number" data-line-number="309"></td>
2001 <td id="LC309" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> composite_sum2_df</td>
2002 </tr>
2003 <tr>
2004 <td id="L310" class="blob-num js-line-number" data-line-number="310"></td>
2005 <td id="LC310" class="blob-code blob-code-inner js-file-line">
2006 </td>
2007 </tr>
2008 <tr>
2009 <td id="L311" class="blob-num js-line-number" data-line-number="311"></td>
2010 <td id="LC311" class="blob-code blob-code-inner js-file-line">
2011 </td>
2012 </tr>
2013 <tr>
2014 <td id="L312" class="blob-num js-line-number" data-line-number="312"></td>
2015 <td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doMultiBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">composite_df</span>): <span class="pl-c"><span class="pl-c">#</span>array of multiple sum2_dfs</span></td>
2016 </tr>
2017 <tr>
2018 <td id="L313" class="blob-num js-line-number" data-line-number="313"></td>
2019 <td id="LC313" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td>
2020 </tr>
2021 <tr>
2022 <td id="L314" class="blob-num js-line-number" data-line-number="314"></td>
2023 <td id="LC314" class="blob-code blob-code-inner js-file-line"> sampnum <span class="pl-k">=</span> <span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span></td>
2024 </tr>
2025 <tr>
2026 <td id="L315" class="blob-num js-line-number" data-line-number="315"></td>
2027 <td id="LC315" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> need to arrange bars</span></td>
2028 </tr>
2029 <tr>
2030 <td id="L316" class="blob-num js-line-number" data-line-number="316"></td>
2031 <td id="LC316" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> number of phylotype = len(composite_df)</span></td>
2032 </tr>
2033 <tr>
2034 <td id="L317" class="blob-num js-line-number" data-line-number="317"></td>
2035 <td id="LC317" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>number of bars = (len(labelist)-1) +1 for space</span></td>
2036 </tr>
2037 <tr>
2038 <td id="L318" class="blob-num js-line-number" data-line-number="318"></td>
2039 <td id="LC318" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> ytick needs to ne</span></td>
2040 </tr>
2041 <tr>
2042 <td id="L319" class="blob-num js-line-number" data-line-number="319"></td>
2043 <td id="LC319" class="blob-code blob-code-inner js-file-line">
2044 </td>
2045 </tr>
2046 <tr>
2047 <td id="L320" class="blob-num js-line-number" data-line-number="320"></td>
2048 <td id="LC320" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">&#39;</span>tab10<span class="pl-pds">&#39;</span></span>)</td>
2049 </tr>
2050 <tr>
2051 <td id="L321" class="blob-num js-line-number" data-line-number="321"></td>
2052 <td id="LC321" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td>
2053 </tr>
2054 <tr>
2055 <td id="L322" class="blob-num js-line-number" data-line-number="322"></td>
2056 <td id="LC322" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptomes. <span class="pl-pds">&quot;</span></span> \</td>
2057 </tr>
2058 <tr>
2059 <td id="L323" class="blob-num js-line-number" data-line-number="323"></td>
2060 <td id="LC323" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">&quot;</span></span> \</td>
2061 </tr>
2062 <tr>
2063 <td id="L324" class="blob-num js-line-number" data-line-number="324"></td>
2064 <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>for combined transcript abundance. <span class="pl-pds">&quot;</span></span> \</td>
2065 </tr>
2066 <tr>
2067 <td id="L325" class="blob-num js-line-number" data-line-number="325"></td>
2068 <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</span></span></td>
2069 </tr>
2070 <tr>
2071 <td id="L326" class="blob-num js-line-number" data-line-number="326"></td>
2072 <td id="LC326" class="blob-code blob-code-inner js-file-line"> width <span class="pl-k">=</span> <span class="pl-c1">0.6</span></td>
2073 </tr>
2074 <tr>
2075 <td id="L327" class="blob-num js-line-number" data-line-number="327"></td>
2076 <td id="LC327" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> np.arange(width<span class="pl-k">*</span>sampnum<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>))</td>
2077 </tr>
2078 <tr>
2079 <td id="L328" class="blob-num js-line-number" data-line-number="328"></td>
2080 <td id="LC328" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(ind)</span></td>
2081 </tr>
2082 <tr>
2083 <td id="L329" class="blob-num js-line-number" data-line-number="329"></td>
2084 <td id="LC329" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span><span class="pl-c1">0.4</span></td>
2085 </tr>
2086 <tr>
2087 <td id="L330" class="blob-num js-line-number" data-line-number="330"></td>
2088 <td id="LC330" class="blob-code blob-code-inner js-file-line">
2089 </td>
2090 </tr>
2091 <tr>
2092 <td id="L331" class="blob-num js-line-number" data-line-number="331"></td>
2093 <td id="LC331" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td>
2094 </tr>
2095 <tr>
2096 <td id="L332" class="blob-num js-line-number" data-line-number="332"></td>
2097 <td id="LC332" class="blob-code blob-code-inner js-file-line">
2098 </td>
2099 </tr>
2100 <tr>
2101 <td id="L333" class="blob-num js-line-number" data-line-number="333"></td>
2102 <td id="LC333" class="blob-code blob-code-inner js-file-line">
2103 </td>
2104 </tr>
2105 <tr>
2106 <td id="L334" class="blob-num js-line-number" data-line-number="334"></td>
2107 <td id="LC334" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> s <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>, <span class="pl-c1">len</span>(labelList)):</td>
2108 </tr>
2109 <tr>
2110 <td id="L335" class="blob-num js-line-number" data-line-number="335"></td>
2111 <td id="LC335" class="blob-code blob-code-inner js-file-line"> ax.barh(ind, composite_df[labelList[s]], width, <span class="pl-v">color</span><span class="pl-k">=</span>palette[s], <span class="pl-v">label</span><span class="pl-k">=</span>labelList[s])</td>
2112 </tr>
2113 <tr>
2114 <td id="L336" class="blob-num js-line-number" data-line-number="336"></td>
2115 <td id="LC336" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> ind <span class="pl-k">+</span> width</td>
2116 </tr>
2117 <tr>
2118 <td id="L337" class="blob-num js-line-number" data-line-number="337"></td>
2119 <td id="LC337" class="blob-code blob-code-inner js-file-line">
2120 </td>
2121 </tr>
2122 <tr>
2123 <td id="L338" class="blob-num js-line-number" data-line-number="338"></td>
2124 <td id="LC338" class="blob-code blob-code-inner js-file-line"> ax.set(<span class="pl-v">yticks</span><span class="pl-k">=</span>np.arange(width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">2</span>)<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>)), <span class="pl-v">yticklabels</span><span class="pl-k">=</span>composite_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>]) <span class="pl-c"><span class="pl-c">#</span> , ylim=[(len(labelList)-1) * width - 1, len(composite_df)])</span></td>
2125 </tr>
2126 <tr>
2127 <td id="L339" class="blob-num js-line-number" data-line-number="339"></td>
2128 <td id="LC339" class="blob-code blob-code-inner js-file-line"> ax.legend()</td>
2129 </tr>
2130 <tr>
2131 <td id="L340" class="blob-num js-line-number" data-line-number="340"></td>
2132 <td id="LC340" class="blob-code blob-code-inner js-file-line">
2133 </td>
2134 </tr>
2135 <tr>
2136 <td id="L341" class="blob-num js-line-number" data-line-number="341"></td>
2137 <td id="LC341" class="blob-code blob-code-inner js-file-line">
2138 </td>
2139 </tr>
2140 <tr>
2141 <td id="L342" class="blob-num js-line-number" data-line-number="342"></td>
2142 <td id="LC342" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>)</td>
2143 </tr>
2144 <tr>
2145 <td id="L343" class="blob-num js-line-number" data-line-number="343"></td>
2146 <td id="LC343" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td>
2147 </tr>
2148 <tr>
2149 <td id="L344" class="blob-num js-line-number" data-line-number="344"></td>
2150 <td id="LC344" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">&#39;</span>Weighted Phylotype Frequency<span class="pl-pds">&#39;</span></span>)</td>
2151 </tr>
2152 <tr>
2153 <td id="L345" class="blob-num js-line-number" data-line-number="345"></td>
2154 <td id="LC345" class="blob-code blob-code-inner js-file-line">
2155 </td>
2156 </tr>
2157 <tr>
2158 <td id="L346" class="blob-num js-line-number" data-line-number="346"></td>
2159 <td id="LC346" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va=&quot;top&quot;, wrap=&quot;True&quot;)</span></td>
2160 </tr>
2161 <tr>
2162 <td id="L347" class="blob-num js-line-number" data-line-number="347"></td>
2163 <td id="LC347" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td>
2164 </tr>
2165 <tr>
2166 <td id="L348" class="blob-num js-line-number" data-line-number="348"></td>
2167 <td id="LC348" class="blob-code blob-code-inner js-file-line">
2168 </td>
2169 </tr>
2170 <tr>
2171 <td id="L349" class="blob-num js-line-number" data-line-number="349"></td>
2172 <td id="LC349" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.92</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td>
2173 </tr>
2174 <tr>
2175 <td id="L350" class="blob-num js-line-number" data-line-number="350"></td>
2176 <td id="LC350" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>True<span class="pl-pds">&#39;</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>left<span class="pl-pds">&#39;</span></span>,)</td>
2177 </tr>
2178 <tr>
2179 <td id="L351" class="blob-num js-line-number" data-line-number="351"></td>
2180 <td id="LC351" class="blob-code blob-code-inner js-file-line">
2181 </td>
2182 </tr>
2183 <tr>
2184 <td id="L352" class="blob-num js-line-number" data-line-number="352"></td>
2185 <td id="LC352" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_phylotypes.png<span class="pl-pds">&quot;</span></span>)</td>
2186 </tr>
2187 <tr>
2188 <td id="L353" class="blob-num js-line-number" data-line-number="353"></td>
2189 <td id="LC353" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdf<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>:</td>
2190 </tr>
2191 <tr>
2192 <td id="L354" class="blob-num js-line-number" data-line-number="354"></td>
2193 <td id="LC354" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>phylotypes.pdf<span class="pl-pds">&quot;</span></span>)</td>
2194 </tr>
2195 <tr>
2196 <td id="L355" class="blob-num js-line-number" data-line-number="355"></td>
2197 <td id="LC355" class="blob-code blob-code-inner js-file-line"> plt.show()</td>
2198 </tr>
2199 <tr>
2200 <td id="L356" class="blob-num js-line-number" data-line-number="356"></td>
2201 <td id="LC356" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td>
2202 </tr>
2203 <tr>
2204 <td id="L357" class="blob-num js-line-number" data-line-number="357"></td>
2205 <td id="LC357" class="blob-code blob-code-inner js-file-line">
2206 </td>
2207 </tr>
2208 <tr>
2209 <td id="L358" class="blob-num js-line-number" data-line-number="358"></td>
2210 <td id="LC358" class="blob-code blob-code-inner js-file-line">
2211 </td>
2212 </tr>
2213 <tr>
2214 <td id="L359" class="blob-num js-line-number" data-line-number="359"></td>
2215 <td id="LC359" class="blob-code blob-code-inner js-file-line">
2216 </td>
2217 </tr>
2218 <tr>
2219 <td id="L360" class="blob-num js-line-number" data-line-number="360"></td>
2220 <td id="LC360" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">sum2_df</span>):</td>
2221 </tr>
2222 <tr>
2223 <td id="L361" class="blob-num js-line-number" data-line-number="361"></td>
2224 <td id="LC361" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">&#39;</span>tab20<span class="pl-pds">&#39;</span></span>)</td>
2225 </tr>
2226 <tr>
2227 <td id="L362" class="blob-num js-line-number" data-line-number="362"></td>
2228 <td id="LC362" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td>
2229 </tr>
2230 <tr>
2231 <td id="L363" class="blob-num js-line-number" data-line-number="363"></td>
2232 <td id="LC363" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptome. <span class="pl-pds">&quot;</span></span> \</td>
2233 </tr>
2234 <tr>
2235 <td id="L364" class="blob-num js-line-number" data-line-number="364"></td>
2236 <td id="LC364" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">&quot;</span></span> \</td>
2237 </tr>
2238 <tr>
2239 <td id="L365" class="blob-num js-line-number" data-line-number="365"></td>
2240 <td id="LC365" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>for combined transcript abundance. <span class="pl-pds">&quot;</span></span> \</td>
2241 </tr>
2242 <tr>
2243 <td id="L366" class="blob-num js-line-number" data-line-number="366"></td>
2244 <td id="LC366" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</span></span></td>
2245 </tr>
2246 <tr>
2247 <td id="L367" class="blob-num js-line-number" data-line-number="367"></td>
2248 <td id="LC367" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get a list of phylotype, create equivalent of saccver, get a list of</span></td>
2249 </tr>
2250 <tr>
2251 <td id="L368" class="blob-num js-line-number" data-line-number="368"></td>
2252 <td id="LC368" class="blob-code blob-code-inner js-file-line"> maxFPKM <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>].max()</td>
2253 </tr>
2254 <tr>
2255 <td id="L369" class="blob-num js-line-number" data-line-number="369"></td>
2256 <td id="LC369" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>].sum()</td>
2257 </tr>
2258 <tr>
2259 <td id="L370" class="blob-num js-line-number" data-line-number="370"></td>
2260 <td id="LC370" class="blob-code blob-code-inner js-file-line">
2261 </td>
2262 </tr>
2263 <tr>
2264 <td id="L371" class="blob-num js-line-number" data-line-number="371"></td>
2265 <td id="LC371" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Normalised<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>], maxFPKM),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
2266 </tr>
2267 <tr>
2268 <td id="L372" class="blob-num js-line-number" data-line-number="372"></td>
2269 <td id="LC372" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Weighted<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>], total),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
2270 </tr>
2271 <tr>
2272 <td id="L373" class="blob-num js-line-number" data-line-number="373"></td>
2273 <td id="LC373" class="blob-code blob-code-inner js-file-line"> pList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>]</td>
2274 </tr>
2275 <tr>
2276 <td id="L374" class="blob-num js-line-number" data-line-number="374"></td>
2277 <td id="LC374" class="blob-code blob-code-inner js-file-line"> phList <span class="pl-k">=</span> []</td>
2278 </tr>
2279 <tr>
2280 <td id="L375" class="blob-num js-line-number" data-line-number="375"></td>
2281 <td id="LC375" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pList:</td>
2282 </tr>
2283 <tr>
2284 <td id="L376" class="blob-num js-line-number" data-line-number="376"></td>
2285 <td id="LC376" class="blob-code blob-code-inner js-file-line"> phList.append(<span class="pl-c1">str</span>(p))</td>
2286 </tr>
2287 <tr>
2288 <td id="L377" class="blob-num js-line-number" data-line-number="377"></td>
2289 <td id="LC377" class="blob-code blob-code-inner js-file-line">
2290 </td>
2291 </tr>
2292 <tr>
2293 <td id="L378" class="blob-num js-line-number" data-line-number="378"></td>
2294 <td id="LC378" class="blob-code blob-code-inner js-file-line"> fList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Weighted<span class="pl-pds">&#39;</span></span>]</td>
2295 </tr>
2296 <tr>
2297 <td id="L379" class="blob-num js-line-number" data-line-number="379"></td>
2298 <td id="LC379" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(phList)<span class="pl-k">*</span><span class="pl-c1">0.3</span></td>
2299 </tr>
2300 <tr>
2301 <td id="L380" class="blob-num js-line-number" data-line-number="380"></td>
2302 <td id="LC380" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td>
2303 </tr>
2304 <tr>
2305 <td id="L381" class="blob-num js-line-number" data-line-number="381"></td>
2306 <td id="LC381" class="blob-code blob-code-inner js-file-line">
2307 </td>
2308 </tr>
2309 <tr>
2310 <td id="L382" class="blob-num js-line-number" data-line-number="382"></td>
2311 <td id="LC382" class="blob-code blob-code-inner js-file-line"> ax.barh(phList, fList, <span class="pl-v">color</span><span class="pl-k">=</span>palette)</td>
2312 </tr>
2313 <tr>
2314 <td id="L383" class="blob-num js-line-number" data-line-number="383"></td>
2315 <td id="LC383" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>)</td>
2316 </tr>
2317 <tr>
2318 <td id="L384" class="blob-num js-line-number" data-line-number="384"></td>
2319 <td id="LC384" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td>
2320 </tr>
2321 <tr>
2322 <td id="L385" class="blob-num js-line-number" data-line-number="385"></td>
2323 <td id="LC385" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">&#39;</span>Weighted Phylotype Frequency<span class="pl-pds">&#39;</span></span>)</td>
2324 </tr>
2325 <tr>
2326 <td id="L386" class="blob-num js-line-number" data-line-number="386"></td>
2327 <td id="LC386" class="blob-code blob-code-inner js-file-line">
2328 </td>
2329 </tr>
2330 <tr>
2331 <td id="L387" class="blob-num js-line-number" data-line-number="387"></td>
2332 <td id="LC387" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va=&quot;top&quot;, wrap=&quot;True&quot;)</span></td>
2333 </tr>
2334 <tr>
2335 <td id="L388" class="blob-num js-line-number" data-line-number="388"></td>
2336 <td id="LC388" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td>
2337 </tr>
2338 <tr>
2339 <td id="L389" class="blob-num js-line-number" data-line-number="389"></td>
2340 <td id="LC389" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td>
2341 </tr>
2342 <tr>
2343 <td id="L390" class="blob-num js-line-number" data-line-number="390"></td>
2344 <td id="LC390" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>True<span class="pl-pds">&#39;</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>left<span class="pl-pds">&#39;</span></span>,)</td>
2345 </tr>
2346 <tr>
2347 <td id="L391" class="blob-num js-line-number" data-line-number="391"></td>
2348 <td id="LC391" class="blob-code blob-code-inner js-file-line">
2349 </td>
2350 </tr>
2351 <tr>
2352 <td id="L392" class="blob-num js-line-number" data-line-number="392"></td>
2353 <td id="LC392" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_phylotypes.png<span class="pl-pds">&quot;</span></span>)</td>
2354 </tr>
2355 <tr>
2356 <td id="L393" class="blob-num js-line-number" data-line-number="393"></td>
2357 <td id="LC393" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdf<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>:</td>
2358 </tr>
2359 <tr>
2360 <td id="L394" class="blob-num js-line-number" data-line-number="394"></td>
2361 <td id="LC394" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>phylotypes.pdf<span class="pl-pds">&quot;</span></span>)</td>
2362 </tr>
2363 <tr>
2364 <td id="L395" class="blob-num js-line-number" data-line-number="395"></td>
2365 <td id="LC395" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.show()</span></td>
2366 </tr>
2367 <tr>
2368 <td id="L396" class="blob-num js-line-number" data-line-number="396"></td>
2369 <td id="LC396" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td>
2370 </tr>
2371 <tr>
2372 <td id="L397" class="blob-num js-line-number" data-line-number="397"></td>
2373 <td id="LC397" class="blob-code blob-code-inner js-file-line">
2374 </td>
2375 </tr>
2376 <tr>
2377 <td id="L398" class="blob-num js-line-number" data-line-number="398"></td>
2378 <td id="LC398" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {&#39;name&#39;:2, &#39;pdfexport&#39;: 3, &#39;refFastq&#39;: 4, &#39;forward&#39;: 5, &#39;reverse&#39;: 6, &#39;html_file&#39;: 7, &#39;html_resource&#39;: 8}</span></td>
2379 </tr>
2380 <tr>
2381 <td id="L399" class="blob-num js-line-number" data-line-number="399"></td>
2382 <td id="LC399" class="blob-code blob-code-inner js-file-line">
2383 </td>
2384 </tr>
2385 <tr>
2386 <td id="L400" class="blob-num js-line-number" data-line-number="400"></td>
2387 <td id="LC400" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptomicProcess</span>(<span class="pl-smi">args</span>,<span class="pl-smi">argdict</span>):</td>
2388 </tr>
2389 <tr>
2390 <td id="L401" class="blob-num js-line-number" data-line-number="401"></td>
2391 <td id="LC401" class="blob-code blob-code-inner js-file-line"> tdict <span class="pl-k">=</span> {}</td>
2392 </tr>
2393 <tr>
2394 <td id="L402" class="blob-num js-line-number" data-line-number="402"></td>
2395 <td id="LC402" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]]</td>
2396 </tr>
2397 <tr>
2398 <td id="L403" class="blob-num js-line-number" data-line-number="403"></td>
2399 <td id="LC403" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>refFastq<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">&#39;</span>refFastq<span class="pl-pds">&#39;</span></span>]]</td>
2400 </tr>
2401 <tr>
2402 <td id="L404" class="blob-num js-line-number" data-line-number="404"></td>
2403 <td id="LC404" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>]]</td>
2404 </tr>
2405 <tr>
2406 <td id="L405" class="blob-num js-line-number" data-line-number="405"></td>
2407 <td id="LC405" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>]]</td>
2408 </tr>
2409 <tr>
2410 <td id="L406" class="blob-num js-line-number" data-line-number="406"></td>
2411 <td id="LC406" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>vivax_trans_database<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&#39;</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">&#39;</span></span></td>
2412 </tr>
2413 <tr>
2414 <td id="L407" class="blob-num js-line-number" data-line-number="407"></td>
2415 <td id="LC407" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdf<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]]</td>
2416 </tr>
2417 <tr>
2418 <td id="L408" class="blob-num js-line-number" data-line-number="408"></td>
2419 <td id="LC408" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>]]</td>
2420 </tr>
2421 <tr>
2422 <td id="L409" class="blob-num js-line-number" data-line-number="409"></td>
2423 <td id="LC409" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]]</td>
2424 </tr>
2425 <tr>
2426 <td id="L410" class="blob-num js-line-number" data-line-number="410"></td>
2427 <td id="LC410" class="blob-code blob-code-inner js-file-line"> </td>
2428 </tr>
2429 <tr>
2430 <td id="L411" class="blob-num js-line-number" data-line-number="411"></td>
2431 <td id="LC411" class="blob-code blob-code-inner js-file-line"> uploadUserReferenceFastq(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>refFastq<span class="pl-pds">&#39;</span></span>])</td>
2432 </tr>
2433 <tr>
2434 <td id="L412" class="blob-num js-line-number" data-line-number="412"></td>
2435 <td id="LC412" class="blob-code blob-code-inner js-file-line"> transcriptMapping(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>], tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>refFastq<span class="pl-pds">&#39;</span></span>], tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>], tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses bowtie</span></td>
2436 </tr>
2437 <tr>
2438 <td id="L413" class="blob-num js-line-number" data-line-number="413"></td>
2439 <td id="LC413" class="blob-code blob-code-inner js-file-line"> processSamFiles(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses samtools</span></td>
2440 </tr>
2441 <tr>
2442 <td id="L414" class="blob-num js-line-number" data-line-number="414"></td>
2443 <td id="LC414" class="blob-code blob-code-inner js-file-line"> transcriptAbundance(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -&gt; ?.cuff/*.*</span></td>
2444 </tr>
2445 <tr>
2446 <td id="L415" class="blob-num js-line-number" data-line-number="415"></td>
2447 <td id="LC415" class="blob-code blob-code-inner js-file-line"> transcriptsForBlast(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>], tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>refFastq<span class="pl-pds">&#39;</span></span>]) <span class="pl-c"><span class="pl-c">#</span>creates name+4blast.fa</span></td>
2448 </tr>
2449 <tr>
2450 <td id="L416" class="blob-num js-line-number" data-line-number="416"></td>
2451 <td id="LC416" class="blob-code blob-code-inner js-file-line"> blastContigs(tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>], tdict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>], <span class="pl-s"><span class="pl-pds">&#39;</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">&#39;</span></span>)</td>
2452 </tr>
2453 <tr>
2454 <td id="L417" class="blob-num js-line-number" data-line-number="417"></td>
2455 <td id="LC417" class="blob-code blob-code-inner js-file-line"> sum_df, sum2_df <span class="pl-k">=</span> combineFPMK(tdict)</td>
2456 </tr>
2457 <tr>
2458 <td id="L418" class="blob-num js-line-number" data-line-number="418"></td>
2459 <td id="LC418" class="blob-code blob-code-inner js-file-line"> doBarChart(tdict, sum2_df)</td>
2460 </tr>
2461 <tr>
2462 <td id="L419" class="blob-num js-line-number" data-line-number="419"></td>
2463 <td id="LC419" class="blob-code blob-code-inner js-file-line"> createHTML(tdict, sum_df)</td>
2464 </tr>
2465 <tr>
2466 <td id="L420" class="blob-num js-line-number" data-line-number="420"></td>
2467 <td id="LC420" class="blob-code blob-code-inner js-file-line">
2468 </td>
2469 </tr>
2470 <tr>
2471 <td id="L421" class="blob-num js-line-number" data-line-number="421"></td>
2472 <td id="LC421" class="blob-code blob-code-inner js-file-line">
2473 </td>
2474 </tr>
2475 <tr>
2476 <td id="L422" class="blob-num js-line-number" data-line-number="422"></td>
2477 <td id="LC422" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>__main__<span class="pl-pds">&quot;</span></span>:</td>
2478 </tr>
2479 <tr>
2480 <td id="L423" class="blob-num js-line-number" data-line-number="423"></td>
2481 <td id="LC423" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">exit</span>()</td>
2482 </tr>
2483 <tr>
2484 <td id="L424" class="blob-num js-line-number" data-line-number="424"></td>
2485 <td id="LC424" class="blob-code blob-code-inner js-file-line">
2486 </td>
2487 </tr>
2488 <tr>
2489 <td id="L425" class="blob-num js-line-number" data-line-number="425"></td>
2490 <td id="LC425" class="blob-code blob-code-inner js-file-line">
2491 </td>
2492 </tr>
2493 </table>
2494
2495 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
2496 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar">
2497 <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg>
2498 </summary>
2499 <details-menu>
2500 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
2501 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li>
2502 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li>
2503 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/johnheap/VAPPER-Galaxy/blame/a4e16d71fe985f389930c02f94354b87d3aabadb/Tryp_V_T.py">View git blame</a></li>
2504 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li>
2505 </ul>
2506 </details-menu>
2507 </details>
2508
2509 </div>
2510
2511 </div>
2512
2513
2514
2515 <details class="details-reset details-overlay details-overlay-dark">
2516 <summary data-hotkey="l" aria-label="Jump to line"></summary>
2517 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
2518 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="&#x2713;" />
2519 <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line&hellip;" aria-label="Jump to line" autofocus>
2520 <button type="submit" class="btn" data-close-dialog>Go</button>
2521 </form> </details-dialog>
2522 </details>
2523
2524
2525
2526 </div>
2527 <div class="modal-backdrop js-touch-events"></div>
2528 </div>
2529
2530 </main>
2531 </div>
2532
2533
2534 </div>
2535
2536
2537 <div class="footer container-lg width-full p-responsive" role="contentinfo">
2538 <div class="position-relative d-flex flex-row-reverse flex-lg-row flex-wrap flex-lg-nowrap flex-justify-center flex-lg-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light ">
2539 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
2540 <li class="mr-3 mr-lg-0">&copy; 2019 <span title="0.75142s from unicorn-74746df85b-zvhqz">GitHub</span>, Inc.</li>
2541 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li>
2542 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li>
2543 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to security, text:security" href="https://github.com/security">Security</a></li>
2544 <li class="mr-3 mr-lg-0"><a href="https://githubstatus.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
2545 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
2546 </ul>
2547
2548 <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com">
2549 <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
2550 </a>
2551 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
2552 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li>
2553 <li class="mr-3 mr-lg-0"><a href="https://github.com/pricing" data-ga-click="Footer, go to Pricing, text:Pricing">Pricing</a></li>
2554 <li class="mr-3 mr-lg-0"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
2555 <li class="mr-3 mr-lg-0"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
2556 <li class="mr-3 mr-lg-0"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
2557 <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>
2558
2559 </ul>
2560 </div>
2561 <div class="d-flex flex-justify-center pb-6">
2562 <span class="f6 text-gray-light"></span>
2563 </div>
2564 </div>
2565
2566
2567
2568 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
2569 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
2570 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
2571 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
2572 </button>
2573 You can’t perform that action at this time.
2574 </div>
2575
2576
2577 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
2578 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
2579
2580 <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script>
2581
2582
2583
2584 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
2585 >
2586 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
2587 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
2588 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
2589 </div>
2590 <template id="site-details-dialog">
2591 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
2592 <summary role="button" aria-label="Close dialog"></summary>
2593 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
2594 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
2595 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
2596 </button>
2597 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
2598 </details-dialog>
2599 </details>
2600 </template>
2601
2602 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
2603 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
2604 </div>
2605 </div>
2606
2607 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
2608
2609 </body>
2610 </html>
2611