8
|
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.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&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&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="99EA:03C4:48319:89CA2:5CF56242" 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="99EA:03C4:48319:89CA2:5CF56242" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" />
|
|
56 <meta name="analytics-location" content="/<user-name>/<repo-name>/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="YzYyMzAwYTYwMTZlZjQ5YWUzNGIzNTY5ZmQ2NTkxYTVmNWQzYzA5NjdiMTY5MDUxNDBjODNkMjI2NjY2NDk3Znx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiI5OUVBOjAzQzQ6NDgzMTk6ODlDQTI6NUNGNTYyNDIiLCJ0aW1lc3RhbXAiOjE1NTk1ODUzNDYsImhvc3QiOiJnaXRodWIuY29tIn0=">
|
|
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="8f60f90a25489bbe59ea08995f73407524f71ec9">
|
|
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.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="{"event_type":"authentication.click","payload":{"location_in_page":"site header","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"99EA:03C4:48319:89CA2:5CF56242","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="2b5b3e285e06f6291d9585d00d3c451a25d337d3be9971ebaefb9cb398fb4ecc" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
|
|
140 Sign 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">→</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">→</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">→</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">→</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 & contribute</h4>
|
|
205 <ul class="list-style-none mb-3">
|
|
206 <li class="edge-item-fix"><a href="/topics" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Topics">Topics</a></li>
|
|
207 <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li>
|
|
208 <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li>
|
|
209 <li class="edge-item-fix"><a href="https://lab.github.com/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Learning lab">Learning Lab</a></li>
|
|
210 <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li>
|
|
211 </ul>
|
|
212
|
|
213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4>
|
|
214 <ul class="list-style-none mb-0">
|
|
215 <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li>
|
|
216 <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li>
|
|
217 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li>
|
|
218 </ul>
|
|
219 </div>
|
|
220 </details>
|
|
221 </li>
|
|
222
|
|
223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
|
|
224 <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a>
|
|
225 </li>
|
|
226
|
|
227 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
|
|
228 <details class="HeaderMenu-details details-overlay details-reset width-full">
|
|
229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
|
|
230 Pricing
|
|
231 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative">
|
|
232 <path d="M1,1l6.2,6L13,1"></path>
|
|
233 </svg>
|
|
234 </summary>
|
|
235
|
|
236 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
|
|
237 <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a>
|
|
238
|
|
239 <ul class="list-style-none mb-3">
|
|
240 <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li>
|
|
241 <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li>
|
|
242 </ul>
|
|
243
|
|
244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
|
|
245 <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li>
|
|
246 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li>
|
|
247 </ul>
|
|
248 </div>
|
|
249 </details>
|
|
250 </li>
|
|
251 </ul>
|
|
252 </nav>
|
|
253
|
|
254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left">
|
|
255 <div class="d-lg-flex mb-3 mb-lg-0">
|
|
256 <div class="header-search flex-self-stretch flex-lg-self-auto mr-0 mr-lg-3 mb-3 mb-lg-0 scoped-search site-scoped-search js-site-search position-relative js-jump-to"
|
|
257 role="combobox"
|
|
258 aria-owns="jump-to-results"
|
|
259 aria-label="Search or jump to"
|
|
260 aria-haspopup="listbox"
|
|
261 aria-expanded="false"
|
|
262 >
|
|
263 <div class="position-relative">
|
|
264 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="139730674" data-scoped-search-url="/johnheap/VAPPER-Galaxy/search" data-unscoped-search-url="/search" action="/johnheap/VAPPER-Galaxy/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" />
|
|
265 <label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container">
|
|
266 <input type="text"
|
|
267 class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable"
|
|
268 data-hotkey="s,/"
|
|
269 name="q"
|
|
270 value=""
|
|
271 placeholder="Search"
|
|
272 data-unscoped-placeholder="Search GitHub"
|
|
273 data-scoped-placeholder="Search"
|
|
274 autocapitalize="off"
|
|
275 aria-autocomplete="list"
|
|
276 aria-controls="jump-to-results"
|
|
277 aria-label="Search"
|
|
278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=UBI6zrTC3YpC0k8lrlu6srLfkSoG1pT6oQPtlColDmhV/VRup2DMPG2/7aV0Ny9S/lUPp8loX+6gx+nMJGy0Tg=="
|
|
279 spellcheck="false"
|
|
280 autocomplete="off"
|
|
281 >
|
|
282 <input type="hidden" class="js-site-search-type-field" name="type" >
|
|
283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
|
|
284
|
|
285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
|
|
286
|
|
287 <ul class="d-none js-jump-to-suggestions-template-container">
|
|
288
|
|
289
|
|
290 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option">
|
|
291 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
|
|
292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
|
|
293 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
|
|
294 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
|
|
295 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
|
|
296 </div>
|
|
297
|
|
298 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
|
|
299
|
|
300 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
|
|
301 </div>
|
|
302
|
|
303 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
|
|
304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
|
|
305 In this repository
|
|
306 </span>
|
|
307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
|
|
308 All GitHub
|
|
309 </span>
|
|
310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
|
|
311 </div>
|
|
312
|
|
313 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
|
|
314 Jump to
|
|
315 <span class="d-inline-block ml-1 v-align-middle">↵</span>
|
|
316 </div>
|
|
317 </a>
|
|
318 </li>
|
|
319
|
|
320 </ul>
|
|
321
|
|
322 <ul class="d-none js-jump-to-no-results-template-container">
|
|
323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2">
|
|
324 <span class="text-gray">No suggested jump to results</span>
|
|
325 </li>
|
|
326 </ul>
|
|
327
|
|
328 <ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container">
|
|
329
|
|
330
|
|
331 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option">
|
|
332 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
|
|
333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
|
|
334 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
|
|
335 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
|
|
336 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
|
|
337 </div>
|
|
338
|
|
339 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
|
|
340
|
|
341 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
|
|
342 </div>
|
|
343
|
|
344 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
|
|
345 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
|
|
346 In this repository
|
|
347 </span>
|
|
348 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
|
|
349 All GitHub
|
|
350 </span>
|
|
351 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
|
|
352 </div>
|
|
353
|
|
354 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
|
|
355 Jump to
|
|
356 <span class="d-inline-block ml-1 v-align-middle">↵</span>
|
|
357 </div>
|
|
358 </a>
|
|
359 </li>
|
|
360
|
|
361
|
|
362
|
|
363 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option">
|
|
364 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
|
|
365 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
|
|
366 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
|
|
367 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
|
|
368 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
|
|
369 </div>
|
|
370
|
|
371 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
|
|
372
|
|
373 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
|
|
374 </div>
|
|
375
|
|
376 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
|
|
377 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
|
|
378 In this repository
|
|
379 </span>
|
|
380 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
|
|
381 All GitHub
|
|
382 </span>
|
|
383 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
|
|
384 </div>
|
|
385
|
|
386 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
|
|
387 Jump to
|
|
388 <span class="d-inline-block ml-1 v-align-middle">↵</span>
|
|
389 </div>
|
|
390 </a>
|
|
391 </li>
|
|
392
|
|
393
|
|
394 </ul>
|
|
395
|
|
396 </div>
|
|
397 </label>
|
|
398 </form> </div>
|
|
399 </div>
|
|
400
|
|
401 </div>
|
|
402
|
|
403 <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"99EA:03C4:48319:89CA2:5CF56242","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="353e8c84f2f18fd0a1d90ebf90d6ebb40ac5c5e056237a6db808426ed2df827e" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FTryp_V.py">
|
|
404 Sign in
|
|
405 </a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"99EA:03C4:48319:89CA2:5CF56242","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="bdb80b4a14c2cfe7081949b2040a1b106c7d08a74465607e57b93d272d86abe7" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
|
|
406 Sign up
|
|
407 </a> </div>
|
|
408 </div>
|
|
409 </div>
|
|
410 </header>
|
|
411
|
|
412 </div>
|
|
413
|
|
414 <div id="start-of-content" class="show-on-focus"></div>
|
|
415
|
|
416
|
|
417 <div id="js-flash-container">
|
|
418
|
|
419 </div>
|
|
420
|
|
421
|
|
422
|
|
423 <div class="application-main " data-commit-hovercards-enabled>
|
|
424 <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class="">
|
|
425 <main >
|
|
426
|
|
427
|
|
428
|
|
429
|
|
430
|
|
431
|
|
432
|
|
433
|
|
434
|
|
435
|
|
436 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav pt-0 pt-lg-4 ">
|
|
437 <div class="repohead-details-container clearfix container-lg p-responsive d-none d-lg-block">
|
|
438
|
|
439 <ul class="pagehead-actions">
|
|
440
|
|
441
|
|
442
|
|
443
|
|
444 <li>
|
|
445
|
|
446 <a class="tooltipped tooltipped-s btn btn-sm btn-with-count" aria-label="You must be signed in to watch a repository" rel="nofollow" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"notification subscription menu watch","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"99EA:03C4:48319:89CA2:5CF56242","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="b295676f7a5aa2600359d0a9a12dea73d6d1d79065846fa803d253aeb67288b7" 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="{"event_type":"authentication.click","payload":{"location_in_page":"star button","repository_id":139730674,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"99EA:03C4:48319:89CA2:5CF56242","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="be81fccdaaef1ee222c24bd87f541a9143695af5afe58fdc55cf7f9fcdce0c0d" 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="{"event_type":"authentication.click","payload":{"location_in_page":"repo details fork button","repository_id":139730674,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"99EA:03C4:48319:89CA2:5CF56242","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="ef29df81d0b2e392154b2f3ca2dd8e8b69cefb4a893ea0cb024d5fc61c1cecf8" 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.py">Permalink</a>
|
|
599
|
|
600 <!-- blob contrib key: blob_contributors:v21:8d85deac8ee1b9a0a5fd911bb3363ca3 -->
|
|
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="✓" /><input type="hidden" name="_method" value="put" /><input type="hidden" name="authenticity_token" value="xU83zWJUsWkPzSMF0IOgnG1IrFBNczqZ5ywsufEIt6CiBdLKPBDb7d2W/3ZrhrWcftJsVQRrfW0knhZqbFdYTQ==" />
|
|
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="{"event_type":"authentication.click","payload":{"location_in_page":"files signup prompt","repository_id":null,"auth_type":"SIGN_UP","client_id":null,"originating_request_id":"99EA:03C4:48319:89CA2:5CF56242","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="487496866b6d5ec6fe4e392744623d3e1520028554d57ba423b792151b7b40ca" 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.py?source_action=show&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.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.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.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.py" class="Box Box--condensed commit-loader">
|
|
667 <div class="Box-body bg-blue-light f6">
|
|
668 Fetching contributors…
|
|
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">
|
|
686 293 lines (233 sloc)
|
|
687 <span class="file-info-divider"></span>
|
|
688 12.2 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.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.py">Blame</a>
|
|
696 <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/Tryp_V.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">"""</span></span></td>
|
|
722 </tr>
|
|
723 <tr>
|
|
724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
|
|
725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td>
|
|
726 </tr>
|
|
727 <tr>
|
|
728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
|
|
729 <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author: John Heap, Computational Biology Facility, UoL</span></td>
|
|
730 </tr>
|
|
731 <tr>
|
|
732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
|
|
733 <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td>
|
|
734 </tr>
|
|
735 <tr>
|
|
736 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
|
|
737 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
|
|
738 </tr>
|
|
739 <tr>
|
|
740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
|
|
741 <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the "License");</span></td>
|
|
742 </tr>
|
|
743 <tr>
|
|
744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
|
|
745 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td>
|
|
746 </tr>
|
|
747 <tr>
|
|
748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
|
|
749 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td>
|
|
750 </tr>
|
|
751 <tr>
|
|
752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
|
|
753 <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
|
|
754 </tr>
|
|
755 <tr>
|
|
756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
|
|
757 <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td>
|
|
758 </tr>
|
|
759 <tr>
|
|
760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
|
|
761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
|
|
762 </tr>
|
|
763 <tr>
|
|
764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
|
|
765 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td>
|
|
766 </tr>
|
|
767 <tr>
|
|
768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
|
|
769 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td>
|
|
770 </tr>
|
|
771 <tr>
|
|
772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
|
|
773 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td>
|
|
774 </tr>
|
|
775 <tr>
|
|
776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
|
|
777 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td>
|
|
778 </tr>
|
|
779 <tr>
|
|
780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
|
|
781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td>
|
|
782 </tr>
|
|
783 <tr>
|
|
784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
|
|
785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
|
|
786 </tr>
|
|
787 <tr>
|
|
788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
|
|
789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td>
|
|
790 </tr>
|
|
791 <tr>
|
|
792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
|
|
793 <td id="LC19" class="blob-code blob-code-inner js-file-line">
|
|
794 </td>
|
|
795 </tr>
|
|
796 <tr>
|
|
797 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
|
|
798 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib <span class="pl-k">as</span> mpl</td>
|
|
799 </tr>
|
|
800 <tr>
|
|
801 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
|
|
802 <td id="LC21" class="blob-code blob-code-inner js-file-line">mpl.use(<span class="pl-s"><span class="pl-pds">'</span>Agg<span class="pl-pds">'</span></span>)</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> shutil</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> pandas <span class="pl-k">as</span> pd</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> os</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">
|
|
832 </td>
|
|
833 </tr>
|
|
834 <tr>
|
|
835 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
|
|
836 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
|
|
837 </tr>
|
|
838 <tr>
|
|
839 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
|
|
840 <td id="LC30" class="blob-code blob-code-inner js-file-line">
|
|
841 </td>
|
|
842 </tr>
|
|
843 <tr>
|
|
844 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
|
|
845 <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>
|
|
846 </tr>
|
|
847 <tr>
|
|
848 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
|
|
849 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">from</span> matplotlib.patches <span class="pl-k">import</span> Patch</td>
|
|
850 </tr>
|
|
851 <tr>
|
|
852 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
|
|
853 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> seaborn <span class="pl-k">as</span> sns</td>
|
|
854 </tr>
|
|
855 <tr>
|
|
856 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
|
|
857 <td id="LC34" class="blob-code blob-code-inner js-file-line">
|
|
858 </td>
|
|
859 </tr>
|
|
860 <tr>
|
|
861 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
|
|
862 <td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">assembleWithVelvet</span>(<span class="pl-smi">name</span>, <span class="pl-smi">kmers</span>, <span class="pl-smi">inslen</span>, <span class="pl-smi">covcut</span>, <span class="pl-smi">fastq1name</span>,<span class="pl-smi">fastq2name</span>):</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"> <span class="pl-c"><span class="pl-c">#</span>argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"</span></td>
|
|
867 </tr>
|
|
868 <tr>
|
|
869 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
|
|
870 <td id="LC37" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>velveth <span class="pl-pds">"</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span> kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span><span class="pl-k">+</span> kmers <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span> -shortPaired -fastq <span class="pl-pds">"</span></span> <span class="pl-k">+</span> fastq1name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span><span class="pl-k">+</span>fastq2name</td>
|
|
871 </tr>
|
|
872 <tr>
|
|
873 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
|
|
874 <td id="LC38" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
|
|
875 </tr>
|
|
876 <tr>
|
|
877 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
|
|
878 <td id="LC39" 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>
|
|
879 </tr>
|
|
880 <tr>
|
|
881 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
|
|
882 <td id="LC40" 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>
|
|
883 </tr>
|
|
884 <tr>
|
|
885 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
|
|
886 <td id="LC41" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in velveth<span class="pl-pds">"</span></span></td>
|
|
887 </tr>
|
|
888 <tr>
|
|
889 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
|
|
890 <td id="LC42" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>velvetg <span class="pl-pds">"</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -exp_cov auto -ins_length <span class="pl-pds">"</span></span><span class="pl-k">+</span>inslen<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -clean yes -ins_length_sd 50 -min_pair_count 20<span class="pl-pds">"</span></span></td>
|
|
891 </tr>
|
|
892 <tr>
|
|
893 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
|
|
894 <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"</span></td>
|
|
895 </tr>
|
|
896 <tr>
|
|
897 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
|
|
898 <td id="LC44" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString</span></td>
|
|
899 </tr>
|
|
900 <tr>
|
|
901 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
|
|
902 <td id="LC45" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
|
|
903 </tr>
|
|
904 <tr>
|
|
905 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
|
|
906 <td id="LC46" 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>
|
|
907 </tr>
|
|
908 <tr>
|
|
909 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
|
|
910 <td id="LC47" 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>
|
|
911 </tr>
|
|
912 <tr>
|
|
913 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
|
|
914 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in velvetg<span class="pl-pds">"</span></span></td>
|
|
915 </tr>
|
|
916 <tr>
|
|
917 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
|
|
918 <td id="LC49" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>//contigs.fa<span class="pl-pds">"</span></span>,name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.fa<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span> my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";</span></td>
|
|
919 </tr>
|
|
920 <tr>
|
|
921 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
|
|
922 <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>ok<span class="pl-pds">"</span></span></td>
|
|
923 </tr>
|
|
924 <tr>
|
|
925 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
|
|
926 <td id="LC51" class="blob-code blob-code-inner js-file-line">
|
|
927 </td>
|
|
928 </tr>
|
|
929 <tr>
|
|
930 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
|
|
931 <td id="LC52" class="blob-code blob-code-inner js-file-line">
|
|
932 </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-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">database</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"> <span class="pl-c1">print</span>(test_name)</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"> <span class="pl-c1">print</span>(database)</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"> <span class="pl-c"><span class="pl-c">#</span>db_path = os.path.dirname(os.path.realpath(__file__))+database</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"> db_path <span class="pl-k">=</span> database</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"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>blastn -db <span class="pl-pds">"</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -query <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.fa -outfmt 10 -out <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span></td>
|
|
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-c1">print</span>(argString)</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"> 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>
|
|
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-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</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"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in blastall<span class="pl-pds">"</span></span></td>
|
|
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"> blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span>)</td>
|
|
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"> <span class="pl-c"><span class="pl-c">#</span>print (blast_df)</span></td>
|
|
981 </tr>
|
|
982 <tr>
|
|
983 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
|
|
984 <td id="LC65" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){</span></td>
|
|
985 </tr>
|
|
986 <tr>
|
|
987 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
|
|
988 <td id="LC66" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore'</span></td>
|
|
989 </tr>
|
|
990 <tr>
|
|
991 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
|
|
992 <td id="LC67" class="blob-code blob-code-inner js-file-line"> blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>mismatch<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>gapopen<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qend<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>sstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>send<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]</td>
|
|
993 </tr>
|
|
994 <tr>
|
|
995 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
|
|
996 <td id="LC68" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]<span class="pl-k">>=</span><span class="pl-c1">98</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">100</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>]<span class="pl-k"><</span><span class="pl-c1">0.001</span>) ]</td>
|
|
997 </tr>
|
|
998 <tr>
|
|
999 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
|
|
1000 <td id="LC69" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]] <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td>
|
|
1001 </tr>
|
|
1002 <tr>
|
|
1003 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
|
|
1004 <td id="LC70" class="blob-code blob-code-inner js-file-line">
|
|
1005 </td>
|
|
1006 </tr>
|
|
1007 <tr>
|
|
1008 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
|
|
1009 <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> blastResult_df</td>
|
|
1010 </tr>
|
|
1011 <tr>
|
|
1012 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
|
|
1013 <td id="LC72" class="blob-code blob-code-inner js-file-line">
|
|
1014 </td>
|
|
1015 </tr>
|
|
1016 <tr>
|
|
1017 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
|
|
1018 <td id="LC73" class="blob-code blob-code-inner js-file-line">
|
|
1019 </td>
|
|
1020 </tr>
|
|
1021 <tr>
|
|
1022 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
|
|
1023 <td id="LC74" class="blob-code blob-code-inner js-file-line">
|
|
1024 </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-k">def</span> <span class="pl-en">getCogsPresent</span>(<span class="pl-smi">blastResult_df</span>,<span class="pl-smi">strain</span>,<span class="pl-smi">cogOrBinList</span>):</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"> blastResult_df.sort_values(<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>,<span class="pl-v">axis</span> <span class="pl-k">=</span> <span class="pl-c1">0</span>, <span class="pl-v">ascending</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">inplace</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"> nodeList <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>].tolist()</td>
|
|
1037 </tr>
|
|
1038 <tr>
|
|
1039 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
|
|
1040 <td id="LC78" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>].tolist()</td>
|
|
1041 </tr>
|
|
1042 <tr>
|
|
1043 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
|
|
1044 <td id="LC79" class="blob-code blob-code-inner js-file-line"> cogSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(cogList) <span class="pl-c"><span class="pl-c">#</span>get unique values</span></td>
|
|
1045 </tr>
|
|
1046 <tr>
|
|
1047 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
|
|
1048 <td id="LC80" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> <span class="pl-c1">sorted</span>(cogSet) <span class="pl-c"><span class="pl-c">#</span>sort them</span></td>
|
|
1049 </tr>
|
|
1050 <tr>
|
|
1051 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
|
|
1052 <td id="LC81" class="blob-code blob-code-inner js-file-line">
|
|
1053 </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"> <span class="pl-c"><span class="pl-c">#</span>print (cogList)</span></td>
|
|
1058 </tr>
|
|
1059 <tr>
|
|
1060 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
|
|
1061 <td id="LC83" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (len(cogList))</span></td>
|
|
1062 </tr>
|
|
1063 <tr>
|
|
1064 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
|
|
1065 <td id="LC84" class="blob-code blob-code-inner js-file-line">
|
|
1066 </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"> thereList <span class="pl-k">=</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"> dataList <span class="pl-k">=</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"> <span class="pl-c"><span class="pl-c">#</span>dir_path = os.path.dirname(os.path.realpath(__file__))</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"> fname <span class="pl-k">=</span> cogOrBinList</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"> cnt <span class="pl-k">=</span> <span class="pl-c1">0</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">with</span> <span class="pl-c1">open</span> (fname) <span class="pl-k">as</span> f:</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"> <span class="pl-k">for</span> line <span class="pl-k">in</span> f:</td>
|
|
1095 </tr>
|
|
1096 <tr>
|
|
1097 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
|
|
1098 <td id="LC92" class="blob-code blob-code-inner js-file-line"> dataList.append(line.rstrip(<span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n\r</span> <span class="pl-pds">'</span></span>))</td>
|
|
1099 </tr>
|
|
1100 <tr>
|
|
1101 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
|
|
1102 <td id="LC93" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line.rstrip(<span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n\r</span> <span class="pl-pds">'</span></span>) <span class="pl-k">in</span> cogList:</td>
|
|
1103 </tr>
|
|
1104 <tr>
|
|
1105 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
|
|
1106 <td id="LC94" class="blob-code blob-code-inner js-file-line"> thereList.append(<span class="pl-s"><span class="pl-pds">'</span>1<span class="pl-pds">'</span></span>)</td>
|
|
1107 </tr>
|
|
1108 <tr>
|
|
1109 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
|
|
1110 <td id="LC95" class="blob-code blob-code-inner js-file-line"> cnt <span class="pl-k">=</span> cnt<span class="pl-k">+</span><span class="pl-c1">1</span></td>
|
|
1111 </tr>
|
|
1112 <tr>
|
|
1113 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
|
|
1114 <td id="LC96" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td>
|
|
1115 </tr>
|
|
1116 <tr>
|
|
1117 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
|
|
1118 <td id="LC97" class="blob-code blob-code-inner js-file-line"> thereList.append(<span class="pl-s"><span class="pl-pds">'</span>0<span class="pl-pds">'</span></span>)</td>
|
|
1119 </tr>
|
|
1120 <tr>
|
|
1121 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
|
|
1122 <td id="LC98" class="blob-code blob-code-inner js-file-line">
|
|
1123 </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"> <span class="pl-c"><span class="pl-c">#</span>print (thereList)</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"> <span class="pl-c"><span class="pl-c">#</span>print (cnt)</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"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>Cog<span class="pl-pds">'</span></span>: dataList, strain: thereList}</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"> presence_df <span class="pl-k">=</span> pd.DataFrame(data)</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"> <span class="pl-c"><span class="pl-c">#</span>print (presence_df)</span></td>
|
|
1144 </tr>
|
|
1145 <tr>
|
|
1146 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
|
|
1147 <td id="LC104" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> presence_df</td>
|
|
1148 </tr>
|
|
1149 <tr>
|
|
1150 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
|
|
1151 <td id="LC105" class="blob-code blob-code-inner js-file-line">
|
|
1152 </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"><span class="pl-k">def</span> <span class="pl-en">addToCurrentData</span>(<span class="pl-smi">cog_df</span>, <span class="pl-smi">name</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"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</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"> j_fname <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax/TvDatabase<span class="pl-c1">.</span>csv<span class="pl-pds">"</span></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"> tv_df <span class="pl-k">=</span> pd.read_csv(j_fname)</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">
|
|
1173 </td>
|
|
1174 </tr>
|
|
1175 <tr>
|
|
1176 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
|
|
1177 <td id="LC111" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> cog_df[name].tolist()</td>
|
|
1178 </tr>
|
|
1179 <tr>
|
|
1180 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
|
|
1181 <td id="LC112" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cogList.insert(0,'Test')</span></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-c"><span class="pl-c">#</span>print (len(tv_df))</span></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-c"><span class="pl-c">#</span>print(len(cogList))</span></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">
|
|
1194 </td>
|
|
1195 </tr>
|
|
1196 <tr>
|
|
1197 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
|
|
1198 <td id="LC116" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(cogList)</span></td>
|
|
1199 </tr>
|
|
1200 <tr>
|
|
1201 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
|
|
1202 <td id="LC117" class="blob-code blob-code-inner js-file-line"> tv_df.loc[:,name]<span class="pl-k">=</span>cogList</td>
|
|
1203 </tr>
|
|
1204 <tr>
|
|
1205 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
|
|
1206 <td id="LC118" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> tv_df</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">
|
|
1211 </td>
|
|
1212 </tr>
|
|
1213 <tr>
|
|
1214 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
|
|
1215 <td id="LC120" class="blob-code blob-code-inner js-file-line">
|
|
1216 </td>
|
|
1217 </tr>
|
|
1218 <tr>
|
|
1219 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
|
|
1220 <td id="LC121" class="blob-code blob-code-inner js-file-line">
|
|
1221 </td>
|
|
1222 </tr>
|
|
1223 <tr>
|
|
1224 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
|
|
1225 <td id="LC122" class="blob-code blob-code-inner js-file-line">
|
|
1226 </td>
|
|
1227 </tr>
|
|
1228 <tr>
|
|
1229 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
|
|
1230 <td id="LC123" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createClusterMap</span>(<span class="pl-smi">tv_df</span>,<span class="pl-smi">name</span>,<span class="pl-smi">html_path</span>,<span class="pl-smi">pdfExport</span>):</td>
|
|
1231 </tr>
|
|
1232 <tr>
|
|
1233 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
|
|
1234 <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>Retrieve Data</span></td>
|
|
1235 </tr>
|
|
1236 <tr>
|
|
1237 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
|
|
1238 <td id="LC125" 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>
|
|
1239 </tr>
|
|
1240 <tr>
|
|
1241 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
|
|
1242 <td id="LC126" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax/geoTv<span class="pl-c1">.</span>csv<span class="pl-pds">"</span></span></td>
|
|
1243 </tr>
|
|
1244 <tr>
|
|
1245 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
|
|
1246 <td id="LC127" class="blob-code blob-code-inner js-file-line"> geo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
|
|
1247 </tr>
|
|
1248 <tr>
|
|
1249 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
|
|
1250 <td id="LC128" class="blob-code blob-code-inner js-file-line"> geo_df.loc[<span class="pl-c1">len</span>(geo_df)] <span class="pl-k">=</span>[name,name,<span class="pl-s"><span class="pl-pds">'</span>k<span class="pl-pds">'</span></span>]</td>
|
|
1251 </tr>
|
|
1252 <tr>
|
|
1253 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
|
|
1254 <td id="LC129" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(geo_df)</td>
|
|
1255 </tr>
|
|
1256 <tr>
|
|
1257 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
|
|
1258 <td id="LC130" class="blob-code blob-code-inner js-file-line">
|
|
1259 </td>
|
|
1260 </tr>
|
|
1261 <tr>
|
|
1262 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
|
|
1263 <td id="LC131" class="blob-code blob-code-inner js-file-line"> myStrains <span class="pl-k">=</span> tv_df.columns.values.tolist() <span class="pl-c"><span class="pl-c">#</span>beware first entry is COG</span></td>
|
|
1264 </tr>
|
|
1265 <tr>
|
|
1266 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
|
|
1267 <td id="LC132" class="blob-code blob-code-inner js-file-line"> myStrains <span class="pl-k">=</span> myStrains[<span class="pl-c1">1</span>:]</td>
|
|
1268 </tr>
|
|
1269 <tr>
|
|
1270 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
|
|
1271 <td id="LC133" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(myStrains)</td>
|
|
1272 </tr>
|
|
1273 <tr>
|
|
1274 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
|
|
1275 <td id="LC134" class="blob-code blob-code-inner js-file-line"> myPal <span class="pl-k">=</span> []</td>
|
|
1276 </tr>
|
|
1277 <tr>
|
|
1278 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
|
|
1279 <td id="LC135" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> s <span class="pl-k">in</span> myStrains:</td>
|
|
1280 </tr>
|
|
1281 <tr>
|
|
1282 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
|
|
1283 <td id="LC136" class="blob-code blob-code-inner js-file-line"> col <span class="pl-k">=</span> geo_df[(geo_df[<span class="pl-s"><span class="pl-pds">'</span>Strain<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> s)][<span class="pl-s"><span class="pl-pds">'</span>colour<span class="pl-pds">'</span></span>].tolist()</td>
|
|
1284 </tr>
|
|
1285 <tr>
|
|
1286 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
|
|
1287 <td id="LC137" class="blob-code blob-code-inner js-file-line"> myPal.append(col[<span class="pl-c1">0</span>])</td>
|
|
1288 </tr>
|
|
1289 <tr>
|
|
1290 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
|
|
1291 <td id="LC138" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(myPal)</td>
|
|
1292 </tr>
|
|
1293 <tr>
|
|
1294 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
|
|
1295 <td id="LC139" class="blob-code blob-code-inner js-file-line"> mycogmap <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>skyblue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>orangered<span class="pl-pds">'</span></span>] <span class="pl-c"><span class="pl-c">#</span> blue absent,red present</span></td>
|
|
1296 </tr>
|
|
1297 <tr>
|
|
1298 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
|
|
1299 <td id="LC140" class="blob-code blob-code-inner js-file-line"> tv_df.set_index(<span class="pl-s"><span class="pl-pds">'</span>COG<span class="pl-pds">'</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
1300 </tr>
|
|
1301 <tr>
|
|
1302 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
|
|
1303 <td id="LC141" class="blob-code blob-code-inner js-file-line"> tv_df <span class="pl-k">=</span> tv_df[tv_df.columns].astype(<span class="pl-c1">float</span>)</td>
|
|
1304 </tr>
|
|
1305 <tr>
|
|
1306 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
|
|
1307 <td id="LC142" class="blob-code blob-code-inner js-file-line">
|
|
1308 </td>
|
|
1309 </tr>
|
|
1310 <tr>
|
|
1311 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
|
|
1312 <td id="LC143" class="blob-code blob-code-inner js-file-line"> cg <span class="pl-k">=</span> sns.clustermap(tv_df, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>ward<span class="pl-pds">'</span></span>, <span class="pl-v">col_colors</span><span class="pl-k">=</span>myPal, <span class="pl-v">cmap</span><span class="pl-k">=</span>mycogmap, <span class="pl-v">yticklabels</span> <span class="pl-k">=</span> <span class="pl-c1">1500</span>, <span class="pl-v">row_cluster</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">linewidths</span> <span class="pl-k">=</span> <span class="pl-c1">0</span>)</td>
|
|
1313 </tr>
|
|
1314 <tr>
|
|
1315 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
|
|
1316 <td id="LC144" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cg = sns.clustermap(tv_df, method='ward', row_cluster=False, linewidths = 0)</span></td>
|
|
1317 </tr>
|
|
1318 <tr>
|
|
1319 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
|
|
1320 <td id="LC145" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td>
|
|
1321 </tr>
|
|
1322 <tr>
|
|
1323 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
|
|
1324 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>xasix ticks and labels.</span></td>
|
|
1325 </tr>
|
|
1326 <tr>
|
|
1327 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
|
|
1328 <td id="LC147" class="blob-code blob-code-inner js-file-line"> ax.xaxis.tick_top() <span class="pl-c"><span class="pl-c">#</span>set ticks at top</span></td>
|
|
1329 </tr>
|
|
1330 <tr>
|
|
1331 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
|
|
1332 <td id="LC148" class="blob-code blob-code-inner js-file-line"> newlabs <span class="pl-k">=</span> []</td>
|
|
1333 </tr>
|
|
1334 <tr>
|
|
1335 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
|
|
1336 <td id="LC149" class="blob-code blob-code-inner js-file-line">
|
|
1337 </td>
|
|
1338 </tr>
|
|
1339 <tr>
|
|
1340 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
|
|
1341 <td id="LC150" class="blob-code blob-code-inner js-file-line"> labs <span class="pl-k">=</span> ax.xaxis.get_ticklabels()</td>
|
|
1342 </tr>
|
|
1343 <tr>
|
|
1344 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
|
|
1345 <td id="LC151" 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>(labs)):</td>
|
|
1346 </tr>
|
|
1347 <tr>
|
|
1348 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
|
|
1349 <td id="LC152" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(labs[i])</td>
|
|
1350 </tr>
|
|
1351 <tr>
|
|
1352 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
|
|
1353 <td id="LC153" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars</span></td>
|
|
1354 </tr>
|
|
1355 <tr>
|
|
1356 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
|
|
1357 <td id="LC154" class="blob-code blob-code-inner js-file-line"> newlabs.append(<span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span> <span class="pl-k">+</span> labs[i].get_text())</td>
|
|
1358 </tr>
|
|
1359 <tr>
|
|
1360 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
|
|
1361 <td id="LC155" class="blob-code blob-code-inner js-file-line"> ax.xaxis.set_ticklabels(newlabs)</td>
|
|
1362 </tr>
|
|
1363 <tr>
|
|
1364 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
|
|
1365 <td id="LC156" class="blob-code blob-code-inner js-file-line">
|
|
1366 </td>
|
|
1367 </tr>
|
|
1368 <tr>
|
|
1369 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
|
|
1370 <td id="LC157" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>labs = ax.xaxis.get_ticklabels()</span></td>
|
|
1371 </tr>
|
|
1372 <tr>
|
|
1373 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
|
|
1374 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>for i in range(0, len(labs)):</span></td>
|
|
1375 </tr>
|
|
1376 <tr>
|
|
1377 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
|
|
1378 <td id="LC159" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(labs[i])</span></td>
|
|
1379 </tr>
|
|
1380 <tr>
|
|
1381 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
|
|
1382 <td id="LC160" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars</span></td>
|
|
1383 </tr>
|
|
1384 <tr>
|
|
1385 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
|
|
1386 <td id="LC161" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(labs[i])</span></td>
|
|
1387 </tr>
|
|
1388 <tr>
|
|
1389 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
|
|
1390 <td id="LC162" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ax.xaxis.set_ticklabels(labs)</span></td>
|
|
1391 </tr>
|
|
1392 <tr>
|
|
1393 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
|
|
1394 <td id="LC163" class="blob-code blob-code-inner js-file-line"> plt.setp(cg.ax_heatmap.xaxis.get_ticklabels(), <span class="pl-v">rotation</span><span class="pl-k">=</span><span class="pl-c1">90</span>) <span class="pl-c"><span class="pl-c">#</span> get x labels printed vertically</span></td>
|
|
1395 </tr>
|
|
1396 <tr>
|
|
1397 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
|
|
1398 <td id="LC164" class="blob-code blob-code-inner js-file-line">
|
|
1399 </td>
|
|
1400 </tr>
|
|
1401 <tr>
|
|
1402 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
|
|
1403 <td id="LC165" class="blob-code blob-code-inner js-file-line"> cg.cax.set_visible(<span class="pl-c1">False</span>)</td>
|
|
1404 </tr>
|
|
1405 <tr>
|
|
1406 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
|
|
1407 <td id="LC166" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td>
|
|
1408 </tr>
|
|
1409 <tr>
|
|
1410 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
|
|
1411 <td id="LC167" class="blob-code blob-code-inner js-file-line"> ax.set_yticklabels(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span>)</td>
|
|
1412 </tr>
|
|
1413 <tr>
|
|
1414 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
|
|
1415 <td id="LC168" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span>)</td>
|
|
1416 </tr>
|
|
1417 <tr>
|
|
1418 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
|
|
1419 <td id="LC169" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td>
|
|
1420 </tr>
|
|
1421 <tr>
|
|
1422 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
|
|
1423 <td id="LC170" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> ax.set_title("Variant antigen profiles of T. vivax genomes.\nDendrogram reflects the VSG repertoire relationships of each strain inferred by the presence and absence of non-universal T. vivax VSG orthologs.", va = "top", wrap = "True")</span></td>
|
|
1424 </tr>
|
|
1425 <tr>
|
|
1426 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
|
|
1427 <td id="LC171" class="blob-code blob-code-inner js-file-line"> b <span class="pl-k">=</span> <span class="pl-c1">len</span>(tv_df)</td>
|
|
1428 </tr>
|
|
1429 <tr>
|
|
1430 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
|
|
1431 <td id="LC172" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(b)</td>
|
|
1432 </tr>
|
|
1433 <tr>
|
|
1434 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
|
|
1435 <td id="LC173" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Figure Legend: The Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ <span class="pl-pds">"</span></span> \</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"> <span class="pl-s"><span class="pl-pds">"</span>showing the <span class="pl-cce">\n</span>combination of present and absent diagnostic cluster of VSG orthologs <span class="pl-pds">"</span></span> \</td>
|
|
1440 </tr>
|
|
1441 <tr>
|
|
1442 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
|
|
1443 <td id="LC175" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>across the sample cohort. <span class="pl-cce">\n</span>Dendrogram reflects the relationships amongst the VSG<span class="pl-pds">"</span></span> \</td>
|
|
1444 </tr>
|
|
1445 <tr>
|
|
1446 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
|
|
1447 <td id="LC176" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span> repertoires of each strain. <span class="pl-pds">"</span></span> \</td>
|
|
1448 </tr>
|
|
1449 <tr>
|
|
1450 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
|
|
1451 <td id="LC177" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Strains were isolated <span class="pl-cce">\n</span>from multiple African countries as shown in the key.<span class="pl-cce">\n</span>Data was produced with the <span class="pl-pds">"</span></span> \</td>
|
|
1452 </tr>
|
|
1453 <tr>
|
|
1454 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
|
|
1455 <td id="LC178" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>'Variant Antigen Profiler' (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td>
|
|
1456 </tr>
|
|
1457 <tr>
|
|
1458 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
|
|
1459 <td id="LC179" class="blob-code blob-code-inner js-file-line">
|
|
1460 </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"> ax.text(<span class="pl-k">-</span><span class="pl-c1">1.5</span>, <span class="pl-c1">len</span>(tv_df) <span class="pl-k">+</span> <span class="pl-c1">8</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"> title,</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"> <span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>left<span class="pl-pds">"</span></span>, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>top<span class="pl-pds">"</span></span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>True<span class="pl-pds">"</span></span>)</td>
|
|
1473 </tr>
|
|
1474 <tr>
|
|
1475 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
|
|
1476 <td id="LC183" class="blob-code blob-code-inner js-file-line"> col <span class="pl-k">=</span> cg.ax_col_dendrogram.get_position()</td>
|
|
1477 </tr>
|
|
1478 <tr>
|
|
1479 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
|
|
1480 <td id="LC184" class="blob-code blob-code-inner js-file-line"> cg.ax_col_dendrogram.set_position([col.x0, col.y0<span class="pl-k">*</span><span class="pl-c1">1.08</span>, col.width, col.height<span class="pl-k">*</span><span class="pl-c1">1.1</span>])</td>
|
|
1481 </tr>
|
|
1482 <tr>
|
|
1483 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
|
|
1484 <td id="LC185" class="blob-code blob-code-inner js-file-line">
|
|
1485 </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"> countryList <span class="pl-k">=</span> pd.unique(geo_df[<span class="pl-s"><span class="pl-pds">'</span>Location<span class="pl-pds">'</span></span>])</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"> colourList <span class="pl-k">=</span> pd.unique(geo_df[<span class="pl-s"><span class="pl-pds">'</span>colour<span class="pl-pds">'</span></span>])</td>
|
|
1494 </tr>
|
|
1495 <tr>
|
|
1496 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
|
|
1497 <td id="LC188" class="blob-code blob-code-inner js-file-line"> legend_elements <span class="pl-k">=</span> [Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>orangered<span class="pl-pds">'</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>COG Present<span class="pl-pds">'</span></span>),</td>
|
|
1498 </tr>
|
|
1499 <tr>
|
|
1500 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
|
|
1501 <td id="LC189" class="blob-code blob-code-inner js-file-line"> Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>skyblue<span class="pl-pds">'</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>COG Absent<span class="pl-pds">'</span></span>)]</td>
|
|
1502 </tr>
|
|
1503 <tr>
|
|
1504 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
|
|
1505 <td id="LC190" class="blob-code blob-code-inner js-file-line">
|
|
1506 </td>
|
|
1507 </tr>
|
|
1508 <tr>
|
|
1509 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
|
|
1510 <td id="LC191" 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>(colourList)):</td>
|
|
1511 </tr>
|
|
1512 <tr>
|
|
1513 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
|
|
1514 <td id="LC192" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>country = <span class="pl-c1">%s</span>, colour = <span class="pl-c1">%s</span><span class="pl-pds">"</span></span> <span class="pl-k">%</span> (countryList[i], colourList[i]))</td>
|
|
1515 </tr>
|
|
1516 <tr>
|
|
1517 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
|
|
1518 <td id="LC193" class="blob-code blob-code-inner js-file-line"> p <span class="pl-k">=</span> Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-c1">str</span>(colourList[i]), <span class="pl-v">label</span><span class="pl-k">=</span>countryList[i])</td>
|
|
1519 </tr>
|
|
1520 <tr>
|
|
1521 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
|
|
1522 <td id="LC194" class="blob-code blob-code-inner js-file-line"> legend_elements.append(p)</td>
|
|
1523 </tr>
|
|
1524 <tr>
|
|
1525 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
|
|
1526 <td id="LC195" class="blob-code blob-code-inner js-file-line">
|
|
1527 </td>
|
|
1528 </tr>
|
|
1529 <tr>
|
|
1530 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
|
|
1531 <td id="LC196" class="blob-code blob-code-inner js-file-line"> ax.legend(<span class="pl-v">handles</span> <span class="pl-k">=</span> legend_elements, <span class="pl-v">bbox_to_anchor</span><span class="pl-k">=</span>(<span class="pl-k">-</span><span class="pl-c1">0.3</span>,<span class="pl-c1">1.2</span>),<span class="pl-v">loc</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>upper left<span class="pl-pds">'</span></span>)</td>
|
|
1532 </tr>
|
|
1533 <tr>
|
|
1534 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
|
|
1535 <td id="LC197" class="blob-code blob-code-inner js-file-line">
|
|
1536 </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">
|
|
1541 </td>
|
|
1542 </tr>
|
|
1543 <tr>
|
|
1544 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
|
|
1545 <td id="LC199" class="blob-code blob-code-inner js-file-line">
|
|
1546 </td>
|
|
1547 </tr>
|
|
1548 <tr>
|
|
1549 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
|
|
1550 <td id="LC200" class="blob-code blob-code-inner js-file-line">
|
|
1551 </td>
|
|
1552 </tr>
|
|
1553 <tr>
|
|
1554 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
|
|
1555 <td id="LC201" class="blob-code blob-code-inner js-file-line">
|
|
1556 </td>
|
|
1557 </tr>
|
|
1558 <tr>
|
|
1559 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
|
|
1560 <td id="LC202" class="blob-code blob-code-inner js-file-line">
|
|
1561 </td>
|
|
1562 </tr>
|
|
1563 <tr>
|
|
1564 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
|
|
1565 <td id="LC203" class="blob-code blob-code-inner js-file-line">
|
|
1566 </td>
|
|
1567 </tr>
|
|
1568 <tr>
|
|
1569 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
|
|
1570 <td id="LC204" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0 ) # get y labels printed horizontally</span></td>
|
|
1571 </tr>
|
|
1572 <tr>
|
|
1573 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
|
|
1574 <td id="LC205" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_col.linkage # linkage matrix for columns</span></td>
|
|
1575 </tr>
|
|
1576 <tr>
|
|
1577 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
|
|
1578 <td id="LC206" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_row.linkage # linkage matrix for rows</span></td>
|
|
1579 </tr>
|
|
1580 <tr>
|
|
1581 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
|
|
1582 <td id="LC207" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.savefig(r"results/" + name + "_heatmap.png")</span></td>
|
|
1583 </tr>
|
|
1584 <tr>
|
|
1585 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
|
|
1586 <td id="LC208" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.savefig(htmlresource + "/heatmap.png")</span></td>
|
|
1587 </tr>
|
|
1588 <tr>
|
|
1589 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
|
|
1590 <td id="LC209" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>if pdf == 'PDF_Yes':</span></td>
|
|
1591 </tr>
|
|
1592 <tr>
|
|
1593 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
|
|
1594 <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.savefig(htmlresource + "/heatmap.pdf")</span></td>
|
|
1595 </tr>
|
|
1596 <tr>
|
|
1597 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
|
|
1598 <td id="LC211" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> shutil.copyfile("heatmap.pdf",heatmapfn) #</span></td>
|
|
1599 </tr>
|
|
1600 <tr>
|
|
1601 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
|
|
1602 <td id="LC212" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.legend()</span></td>
|
|
1603 </tr>
|
|
1604 <tr>
|
|
1605 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
|
|
1606 <td id="LC213" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> html_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_clustermap.png<span class="pl-pds">"</span></span></td>
|
|
1607 </tr>
|
|
1608 <tr>
|
|
1609 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
|
|
1610 <td id="LC214" class="blob-code blob-code-inner js-file-line"> cg.savefig(fname)</td>
|
|
1611 </tr>
|
|
1612 <tr>
|
|
1613 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
|
|
1614 <td id="LC215" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> pdfExport <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td>
|
|
1615 </tr>
|
|
1616 <tr>
|
|
1617 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
|
|
1618 <td id="LC216" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> html_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_clustermap.pdf<span class="pl-pds">"</span></span></td>
|
|
1619 </tr>
|
|
1620 <tr>
|
|
1621 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
|
|
1622 <td id="LC217" class="blob-code blob-code-inner js-file-line"> cg.savefig(fname)</td>
|
|
1623 </tr>
|
|
1624 <tr>
|
|
1625 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
|
|
1626 <td id="LC218" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
|
|
1627 </tr>
|
|
1628 <tr>
|
|
1629 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
|
|
1630 <td id="LC219" class="blob-code blob-code-inner js-file-line">
|
|
1631 </td>
|
|
1632 </tr>
|
|
1633 <tr>
|
|
1634 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
|
|
1635 <td id="LC220" 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">name</span>,<span class="pl-smi">htmlfn</span>,<span class="pl-smi">htmlPath</span>):</td>
|
|
1636 </tr>
|
|
1637 <tr>
|
|
1638 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
|
|
1639 <td id="LC221" 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>
|
|
1640 </tr>
|
|
1641 <tr>
|
|
1642 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
|
|
1643 <td id="LC222" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td>
|
|
1644 </tr>
|
|
1645 <tr>
|
|
1646 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
|
|
1647 <td id="LC223" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> name</td>
|
|
1648 </tr>
|
|
1649 <tr>
|
|
1650 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
|
|
1651 <td id="LC224" class="blob-code blob-code-inner js-file-line">
|
|
1652 </td>
|
|
1653 </tr>
|
|
1654 <tr>
|
|
1655 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
|
|
1656 <td id="LC225" class="blob-code blob-code-inner js-file-line">
|
|
1657 </td>
|
|
1658 </tr>
|
|
1659 <tr>
|
|
1660 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
|
|
1661 <td id="LC226" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">'</span><p> <h3>The Heat Map and Dendrogram</h3></p><span class="pl-pds">'</span></span></td>
|
|
1662 </tr>
|
|
1663 <tr>
|
|
1664 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
|
|
1665 <td id="LC227" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_clustermap.png' alt='Cog Clustermap' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td>
|
|
1666 </tr>
|
|
1667 <tr>
|
|
1668 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
|
|
1669 <td id="LC228" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
|
|
1670 </tr>
|
|
1671 <tr>
|
|
1672 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
|
|
1673 <td id="LC229" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(htmlString)</td>
|
|
1674 </tr>
|
|
1675 <tr>
|
|
1676 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
|
|
1677 <td id="LC230" class="blob-code blob-code-inner js-file-line">
|
|
1678 </td>
|
|
1679 </tr>
|
|
1680 <tr>
|
|
1681 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
|
|
1682 <td id="LC231" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(htmlfn, <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td>
|
|
1683 </tr>
|
|
1684 <tr>
|
|
1685 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
|
|
1686 <td id="LC232" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
|
|
1687 </tr>
|
|
1688 <tr>
|
|
1689 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
|
|
1690 <td id="LC233" class="blob-code blob-code-inner js-file-line">
|
|
1691 </td>
|
|
1692 </tr>
|
|
1693 <tr>
|
|
1694 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
|
|
1695 <td id="LC234" class="blob-code blob-code-inner js-file-line">
|
|
1696 </td>
|
|
1697 </tr>
|
|
1698 <tr>
|
|
1699 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
|
|
1700 <td id="LC235" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">vivax_assemble</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
|
|
1701 </tr>
|
|
1702 <tr>
|
|
1703 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
|
|
1704 <td id="LC236" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10}</span></td>
|
|
1705 </tr>
|
|
1706 <tr>
|
|
1707 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
|
|
1708 <td id="LC237" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assembleWithVelvet("V2_Test", '65', '400', '5', "data/TviBrRp.1.clean", "data/TviBrRp.2.clean")</span></td>
|
|
1709 </tr>
|
|
1710 <tr>
|
|
1711 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
|
|
1712 <td id="LC238" class="blob-code blob-code-inner js-file-line">
|
|
1713 </td>
|
|
1714 </tr>
|
|
1715 <tr>
|
|
1716 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
|
|
1717 <td id="LC239" class="blob-code blob-code-inner js-file-line"> vivaxPath <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax<span class="pl-pds">"</span></span></td>
|
|
1718 </tr>
|
|
1719 <tr>
|
|
1720 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
|
|
1721 <td id="LC240" class="blob-code blob-code-inner js-file-line"> assembleWithVelvet(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>kmers<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>]],</td>
|
|
1722 </tr>
|
|
1723 <tr>
|
|
1724 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
|
|
1725 <td id="LC241" class="blob-code blob-code-inner js-file-line"> args[dict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]])</td>
|
|
1726 </tr>
|
|
1727 <tr>
|
|
1728 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
|
|
1729 <td id="LC242" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td>
|
|
1730 </tr>
|
|
1731 <tr>
|
|
1732 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
|
|
1733 <td id="LC243" class="blob-code blob-code-inner js-file-line"> orthPresence_df <span class="pl-k">=</span> getCogsPresent(blastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td>
|
|
1734 </tr>
|
|
1735 <tr>
|
|
1736 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
|
|
1737 <td id="LC244" class="blob-code blob-code-inner js-file-line">
|
|
1738 </td>
|
|
1739 </tr>
|
|
1740 <tr>
|
|
1741 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
|
|
1742 <td id="LC245" class="blob-code blob-code-inner js-file-line"> binBlastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td>
|
|
1743 </tr>
|
|
1744 <tr>
|
|
1745 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
|
|
1746 <td id="LC246" class="blob-code blob-code-inner js-file-line"> binPresence_df <span class="pl-k">=</span> getCogsPresent(binBlastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td>
|
|
1747 </tr>
|
|
1748 <tr>
|
|
1749 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
|
|
1750 <td id="LC247" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> orthPresence_df.append(binPresence_df, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
1751 </tr>
|
|
1752 <tr>
|
|
1753 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
|
|
1754 <td id="LC248" class="blob-code blob-code-inner js-file-line">
|
|
1755 </td>
|
|
1756 </tr>
|
|
1757 <tr>
|
|
1758 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
|
|
1759 <td id="LC249" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]] <span class="pl-k">+</span>args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_cogspresent.csv<span class="pl-pds">"</span></span></td>
|
|
1760 </tr>
|
|
1761 <tr>
|
|
1762 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
|
|
1763 <td id="LC250" class="blob-code blob-code-inner js-file-line"> cogPresence_df.to_csv(fname)</td>
|
|
1764 </tr>
|
|
1765 <tr>
|
|
1766 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
|
|
1767 <td id="LC251" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td>
|
|
1768 </tr>
|
|
1769 <tr>
|
|
1770 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
|
|
1771 <td id="LC252" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td>
|
|
1772 </tr>
|
|
1773 <tr>
|
|
1774 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
|
|
1775 <td id="LC253" class="blob-code blob-code-inner js-file-line"> createHTML(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]])</td>
|
|
1776 </tr>
|
|
1777 <tr>
|
|
1778 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
|
|
1779 <td id="LC254" class="blob-code blob-code-inner js-file-line">
|
|
1780 </td>
|
|
1781 </tr>
|
|
1782 <tr>
|
|
1783 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
|
|
1784 <td id="LC255" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">test_cluster</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
|
|
1785 </tr>
|
|
1786 <tr>
|
|
1787 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
|
|
1788 <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span> (<span class="pl-s"><span class="pl-pds">"</span>name: <span class="pl-c1">%s</span><span class="pl-pds">"</span></span>,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]])</td>
|
|
1789 </tr>
|
|
1790 <tr>
|
|
1791 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
|
|
1792 <td id="LC257" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span>test_cogspresent.csv<span class="pl-pds">"</span></span>)</td>
|
|
1793 </tr>
|
|
1794 <tr>
|
|
1795 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
|
|
1796 <td id="LC258" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(cogPresence_df)</td>
|
|
1797 </tr>
|
|
1798 <tr>
|
|
1799 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
|
|
1800 <td id="LC259" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td>
|
|
1801 </tr>
|
|
1802 <tr>
|
|
1803 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
|
|
1804 <td id="LC260" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td>
|
|
1805 </tr>
|
|
1806 <tr>
|
|
1807 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
|
|
1808 <td id="LC261" class="blob-code blob-code-inner js-file-line">
|
|
1809 </td>
|
|
1810 </tr>
|
|
1811 <tr>
|
|
1812 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
|
|
1813 <td id="LC262" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">vivax_contigs</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
|
|
1814 </tr>
|
|
1815 <tr>
|
|
1816 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
|
|
1817 <td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6}</span></td>
|
|
1818 </tr>
|
|
1819 <tr>
|
|
1820 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
|
|
1821 <td id="LC264" class="blob-code blob-code-inner js-file-line">
|
|
1822 </td>
|
|
1823 </tr>
|
|
1824 <tr>
|
|
1825 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
|
|
1826 <td id="LC265" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>test_cluster(args,dict)</span></td>
|
|
1827 </tr>
|
|
1828 <tr>
|
|
1829 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
|
|
1830 <td id="LC266" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>return;</span></td>
|
|
1831 </tr>
|
|
1832 <tr>
|
|
1833 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
|
|
1834 <td id="LC267" class="blob-code blob-code-inner js-file-line">
|
|
1835 </td>
|
|
1836 </tr>
|
|
1837 <tr>
|
|
1838 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
|
|
1839 <td id="LC268" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>subprocess.call('echo $PATH',shell = True)</span></td>
|
|
1840 </tr>
|
|
1841 <tr>
|
|
1842 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
|
|
1843 <td id="LC269" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>sys.exit(1)</span></td>
|
|
1844 </tr>
|
|
1845 <tr>
|
|
1846 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
|
|
1847 <td id="LC270" class="blob-code blob-code-inner js-file-line">
|
|
1848 </td>
|
|
1849 </tr>
|
|
1850 <tr>
|
|
1851 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
|
|
1852 <td id="LC271" class="blob-code blob-code-inner js-file-line"> vivaxPath <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax<span class="pl-pds">"</span></span></td>
|
|
1853 </tr>
|
|
1854 <tr>
|
|
1855 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
|
|
1856 <td id="LC272" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(args[dict[<span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.fa<span class="pl-pds">"</span></span>)</td>
|
|
1857 </tr>
|
|
1858 <tr>
|
|
1859 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
|
|
1860 <td id="LC273" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td>
|
|
1861 </tr>
|
|
1862 <tr>
|
|
1863 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
|
|
1864 <td id="LC274" class="blob-code blob-code-inner js-file-line"> orthPresence_df <span class="pl-k">=</span> getCogsPresent(blastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td>
|
|
1865 </tr>
|
|
1866 <tr>
|
|
1867 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
|
|
1868 <td id="LC275" class="blob-code blob-code-inner js-file-line">
|
|
1869 </td>
|
|
1870 </tr>
|
|
1871 <tr>
|
|
1872 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
|
|
1873 <td id="LC276" class="blob-code blob-code-inner js-file-line"> binBlastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td>
|
|
1874 </tr>
|
|
1875 <tr>
|
|
1876 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
|
|
1877 <td id="LC277" class="blob-code blob-code-inner js-file-line"> binPresence_df <span class="pl-k">=</span> getCogsPresent(binBlastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td>
|
|
1878 </tr>
|
|
1879 <tr>
|
|
1880 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
|
|
1881 <td id="LC278" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> orthPresence_df.append(binPresence_df, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
|
|
1882 </tr>
|
|
1883 <tr>
|
|
1884 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
|
|
1885 <td id="LC279" class="blob-code blob-code-inner js-file-line">
|
|
1886 </td>
|
|
1887 </tr>
|
|
1888 <tr>
|
|
1889 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
|
|
1890 <td id="LC280" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_cogspresent.csv<span class="pl-pds">"</span></span></td>
|
|
1891 </tr>
|
|
1892 <tr>
|
|
1893 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
|
|
1894 <td id="LC281" class="blob-code blob-code-inner js-file-line"> cogPresence_df.to_csv(fname)</td>
|
|
1895 </tr>
|
|
1896 <tr>
|
|
1897 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
|
|
1898 <td id="LC282" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td>
|
|
1899 </tr>
|
|
1900 <tr>
|
|
1901 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
|
|
1902 <td id="LC283" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td>
|
|
1903 </tr>
|
|
1904 <tr>
|
|
1905 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
|
|
1906 <td id="LC284" class="blob-code blob-code-inner js-file-line"> createHTML(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]])</td>
|
|
1907 </tr>
|
|
1908 <tr>
|
|
1909 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
|
|
1910 <td id="LC285" class="blob-code blob-code-inner js-file-line">
|
|
1911 </td>
|
|
1912 </tr>
|
|
1913 <tr>
|
|
1914 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
|
|
1915 <td id="LC286" class="blob-code blob-code-inner js-file-line">
|
|
1916 </td>
|
|
1917 </tr>
|
|
1918 <tr>
|
|
1919 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
|
|
1920 <td id="LC287" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>__main__<span class="pl-pds">"</span></span>:</td>
|
|
1921 </tr>
|
|
1922 <tr>
|
|
1923 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
|
|
1924 <td id="LC288" class="blob-code blob-code-inner js-file-line"> sys.exit()</td>
|
|
1925 </tr>
|
|
1926 <tr>
|
|
1927 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
|
|
1928 <td id="LC289" class="blob-code blob-code-inner js-file-line">
|
|
1929 </td>
|
|
1930 </tr>
|
|
1931 <tr>
|
|
1932 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
|
|
1933 <td id="LC290" class="blob-code blob-code-inner js-file-line">
|
|
1934 </td>
|
|
1935 </tr>
|
|
1936 <tr>
|
|
1937 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
|
|
1938 <td id="LC291" class="blob-code blob-code-inner js-file-line">
|
|
1939 </td>
|
|
1940 </tr>
|
|
1941 <tr>
|
|
1942 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
|
|
1943 <td id="LC292" class="blob-code blob-code-inner js-file-line">
|
|
1944 </td>
|
|
1945 </tr>
|
|
1946 </table>
|
|
1947
|
|
1948 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
|
|
1949 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar">
|
|
1950 <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>
|
|
1951 </summary>
|
|
1952 <details-menu>
|
|
1953 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
|
|
1954 <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>
|
|
1955 <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>
|
|
1956 <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.py">View git blame</a></li>
|
|
1957 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li>
|
|
1958 </ul>
|
|
1959 </details-menu>
|
|
1960 </details>
|
|
1961
|
|
1962 </div>
|
|
1963
|
|
1964 </div>
|
|
1965
|
|
1966
|
|
1967
|
|
1968 <details class="details-reset details-overlay details-overlay-dark">
|
|
1969 <summary data-hotkey="l" aria-label="Jump to line"></summary>
|
|
1970 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
|
|
1971 <!-- '"` --><!-- </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="✓" />
|
|
1972 <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus>
|
|
1973 <button type="submit" class="btn" data-close-dialog>Go</button>
|
|
1974 </form> </details-dialog>
|
|
1975 </details>
|
|
1976
|
|
1977
|
|
1978
|
|
1979 </div>
|
|
1980 <div class="modal-backdrop js-touch-events"></div>
|
|
1981 </div>
|
|
1982
|
|
1983 </main>
|
|
1984 </div>
|
|
1985
|
|
1986
|
|
1987 </div>
|
|
1988
|
|
1989
|
|
1990 <div class="footer container-lg width-full p-responsive" role="contentinfo">
|
|
1991 <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 ">
|
|
1992 <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">
|
|
1993 <li class="mr-3 mr-lg-0">© 2019 <span title="0.20802s from unicorn-74746df85b-kqc5g">GitHub</span>, Inc.</li>
|
|
1994 <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>
|
|
1995 <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>
|
|
1996 <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>
|
|
1997 <li class="mr-3 mr-lg-0"><a href="https://githubstatus.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
|
|
1998 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
|
|
1999 </ul>
|
|
2000
|
|
2001 <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com">
|
|
2002 <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>
|
|
2003 </a>
|
|
2004 <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">
|
|
2005 <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>
|
|
2006 <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>
|
|
2007 <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>
|
|
2008 <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>
|
|
2009 <li class="mr-3 mr-lg-0"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
|
|
2010 <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>
|
|
2011
|
|
2012 </ul>
|
|
2013 </div>
|
|
2014 <div class="d-flex flex-justify-center pb-6">
|
|
2015 <span class="f6 text-gray-light"></span>
|
|
2016 </div>
|
|
2017 </div>
|
|
2018
|
|
2019
|
|
2020
|
|
2021 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
|
|
2022 <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>
|
|
2023 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
|
|
2024 <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>
|
|
2025 </button>
|
|
2026 You can’t perform that action at this time.
|
|
2027 </div>
|
|
2028
|
|
2029
|
|
2030 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
|
|
2031 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
|
|
2032
|
|
2033 <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script>
|
|
2034
|
|
2035
|
|
2036
|
|
2037 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
|
|
2038 >
|
|
2039 <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>
|
|
2040 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
|
|
2041 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
|
|
2042 </div>
|
|
2043 <template id="site-details-dialog">
|
|
2044 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
|
|
2045 <summary role="button" aria-label="Close dialog"></summary>
|
|
2046 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
|
|
2047 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
|
|
2048 <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>
|
|
2049 </button>
|
|
2050 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
|
|
2051 </details-dialog>
|
|
2052 </details>
|
|
2053 </template>
|
|
2054
|
|
2055 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
|
|
2056 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
|
|
2057 </div>
|
|
2058 </div>
|
|
2059
|
|
2060 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
|
|
2061
|
|
2062 </body>
|
|
2063 </html>
|
|
2064
|